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4p9h

Crystal structure of 8ANC195 Fab in complex with gp120 of 93TH057 HIV-1 and soluble CD4 D1D2

Method: X-RAY DIFFRACTION Dmax: 118.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

T-cell surface glycoprotein CD4

Homo sapiens

UniProt P01730

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 4 其他Polymer 6 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 26–207 Fragment：CD4 D1D2 Mutation：K75T Envelope glycoprotein gp160 × 1 （Q0ED31） Fab heavy chain × 1 Fab light chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 BEN BENZAMIDINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.3；298 K；PEG 3350, HEPES, benzamidine Resolution 3.00 Å R-free 0.272

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4P9H Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CDH STRUCTURES OF AN HIV AND MHC BINDING FRAGMENT FROM HUMAN CD4 AS REFINED IN TWO CRYSTAL LATTICES Deposited 1994-01-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 26–203（178 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1CDI STRUCTURES OF AN HIV AND MHC BINDING FRAGMENT FROM HUMAN CD4 AS REFINED IN TWO CRYSTAL LATTICES Deposited 1994-01-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 23–203（181 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.90 Å
1CDJ STRUCTURE OF T-CELL SURFACE GLYCOPROTEIN CD4 Deposited 1996-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–203（178 aa） Fragment：D1D2 FRAGMENT
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
1CDU STRUCTURE OF T-CELL SURFACE GLYCOPROTEIN CD4 MUTANT WITH PHE 43 REPLACED BY VAL Deposited 1996-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–203（178 aa） Fragment：D1D2 FRAGMENT
Mutation：F43V No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å
1CDY STRUCTURE OF T-CELL SURFACE GLYCOPROTEIN CD4 MUTANT WITH GLY 47 REPLACED BY SER Deposited 1996-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–203（178 aa） Fragment：D1D2 FRAGMENT
Mutation：G47S No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
1G9M HIV-1 HXBC2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B Deposited 2000-11-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 26–210（185 aa） Fragment：D1D2, N-TERMINAL TWO DOMAIN FRAGMENT
Mutation：S184N, I185T NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 IPA ISOPROPYL ALCOHOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；VAPOUR DIFFUSION CRYSTALLIZATION: 0.5 UL OF PROTEIN (~10MG/ML IN 350 MM NACL, 5 MM TRISCL PH 7.0) + 0.4 UL OF 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, 0.0075% SEAPREP AGAROSE, PH 6.4 OVER A RESERVOIR OF 0.35 M NACL, 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, PH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.330
1G9N HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B Deposited 2000-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 26–210（185 aa） Fragment：D1D2, N-TERMINAL TWO DOMAIN FRAGMENT
Mutation：S184N, I185T NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；293 K；VAPOUR DIFFUSION CRYSTALLIZATION: 0.5 UL OF PROTEIN (5 MG/ML IN 0.35 M NACL, 0.005 M TRIS CL PH 7.0) + 0.35 UL OF RESERVOIR (50 UL OF NA ACETATE pH 4.5 + 250 UL OF HAMPTON CRYSTAL SCREEN REAGENT 18 + 126 UL OF ETHANOL + 292 UL OF WATER), pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.295
1GC1 HIV-1 GP120 CORE COMPLEXED WITH CD4 AND A NEUTRALIZING HUMAN ANTIBODY Deposited 1998-06-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 26–210（185 aa） Fragment：D1D2, N-TERMINAL TWO DOMAIN FRAGMENT
Mutation：S184N, I185T NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；VAPOUR DIFFUSION CRYSTALLIZATION: 0.5 UL OF PROTEIN (~10MG/ML IN 350 MM NACL, 5 MM TRISCL PH 7.0) + 0.4 UL OF 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, 0.0075% SEAPREP AGAROSE, PH 6.4 OVER A RESERVOIR OF 0.35 M NACL, 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, PH 6.4, vapor diffusion
Resolution 2.50 Å R-free 0.302
1JL4 CRYSTAL STRUCTURE OF THE HUMAN CD4 N-TERMINAL TWO DOMAIN FRAGMENT COMPLEXED TO A CLASS II MHC MOLECULE Deposited 2001-07-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 26–203（178 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；297 K；17% PEG 4,000/0.2M Li2SO4/0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Resolution 4.30 Å R-free 0.453
1Q68 Solution structure of T-cell surface glycoprotein CD4 and Proto-oncogene tyrosine-protein kinase LCK fragments Deposited 2003-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 421–458（38 aa） Fragment：residues 421-458
Mutation：M407L ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 5.1；298 K；Pressure ambient
NMR sample composition 0.5 mM CD4-Lck-Zn2+, U-15N,13C; 20 mM acetate, 20 mM NaCl, 0.15% beta-mercaptoethanol | 95% H2O/5% D2O
NMR sample composition 0.5 mM CD4-Lck-Zn2+, U-15N; 20 mM acetate, 20 mM NaCl, 0.15% beta-mercaptoethanol | 95% H2O/5% D2O
NMR sample composition 0.5 mM CD4-Lck-Zn2+; 20 mM acetate, 20 mM NaCl, 0.15% beta-mercaptoethanol | 100% D2O
NMR sample composition 1.0 mM CD4-Lck-Cd2+; 20 mM acetate, 20 mM NaCl, 0.15% beta-mercaptoethanol | 100% D2O
Resolution not provided
1RZJ HIV-1 HXBC2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B Deposited 2003-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 26–210（185 aa） Fragment：D1D2, N-TERMINAL TWO DOMAIN FRAGMENT
Mutation：S184N, I185T NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 IPA ISOPROPYL ALCOHOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；0.5 UL OF PROTEIN (~10MG/ML IN 350 MM NACL, 5 MM TRISCL PH 7.0) + 0.4 UL OF 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, 0.0075% SEAPREP AGAROSE, PH 6.4 OVER A RESERVOIR OF 0.35 M NACL, 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, PH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.323
1RZK HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B Deposited 2003-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 26–210（185 aa） Fragment：D1D2, N-TERMINAL TWO DOMAIN FRAGMENT
Mutation：S184N, I185T NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；293 K；0.5 UL OF PROTEIN (5 MG/ML IN 0.35 M NACL, 0.005 M TRIS CL PH 7.0) + 0.35 UL OF RESERVOIR (50 UL OF NA ACETATE PH 4.5 + 250 UL OF HAMPTON CRYSTAL SCREEN REAGENT 18 + 126 UL OF ETHANOL + 292 UL OF WATER), pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.297
1WBR SOLUTION STRUCTURE OF THE HUMAN CD4 (403-419) RECEPTOR PEPTIDE, NMR, 32 STRUCTURES Deposited 1996-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 428–444（17 aa） Fragment：403 - 419
Mutation：N-TERMINUS IS ACETYLATED, C-TERMINUS IS AMIDATED Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K
Resolution not provided
1WIO STRUCTURE OF T-CELL SURFACE GLYCOPROTEIN CD4, TETRAGONAL CRYSTAL FORM Deposited 1996-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–388（363 aa） Fragment：EXTRACELLULAR FRAGMENT
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.90 Å R-free 0.351
1WIO STRUCTURE OF T-CELL SURFACE GLYCOPROTEIN CD4, TETRAGONAL CRYSTAL FORM Deposited 1996-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 26–388（363 aa） Fragment：EXTRACELLULAR FRAGMENT
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.90 Å R-free 0.351
1WIP STRUCTURE OF T-CELL SURFACE GLYCOPROTEIN CD4, MONOCLINIC CRYSTAL FORM Deposited 1996-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–388（363 aa） Fragment：EXTRACELLULAR FRAGMENT
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 4.00 Å R-free 0.427
1WIP STRUCTURE OF T-CELL SURFACE GLYCOPROTEIN CD4, MONOCLINIC CRYSTAL FORM Deposited 1996-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 26–388（363 aa） Fragment：EXTRACELLULAR FRAGMENT
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 4.00 Å R-free 0.427
1WIQ STRUCTURE OF T-CELL SURFACE GLYCOPROTEIN CD4, TRIGONAL CRYSTAL FORM Deposited 1996-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–388（363 aa） Fragment：EXTRACELLULAR FRAGMENT
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 5.00 Å R-free 0.442
1WIQ STRUCTURE OF T-CELL SURFACE GLYCOPROTEIN CD4, TRIGONAL CRYSTAL FORM Deposited 1996-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 26–388（363 aa） Fragment：EXTRACELLULAR FRAGMENT
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 5.00 Å R-free 0.442
2B4C Crystal structure of HIV-1 JR-FL gp120 core protein containing the third variable region (V3) complexed with CD4 and the X5 antibody Deposited 2005-09-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 26–206（181 aa） Fragment：D1D2, N-TERMINAL TWO DOMAIN FRAGMENT
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 SO4 SULFATE ION × 5 XYL Xylitol × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；293 K；ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 5.50
Resolution 3.30 Å R-free 0.349
2B4C Crystal structure of HIV-1 JR-FL gp120 core protein containing the third variable region (V3) complexed with CD4 and the X5 antibody Deposited 2005-09-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain C 26–206（181 aa） Fragment：D1D2, N-TERMINAL TWO DOMAIN FRAGMENT
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 SO4 SULFATE ION × 20 XYL Xylitol × 12 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；293 K；ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 5.50
Resolution 3.30 Å R-free 0.349
2KLU NMR structure of the transmembrane and cytoplasmic domains of human CD4 Deposited 2009-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 397–458（62 aa） Fragment：UNP residues 397-458
Mutation：C394S,C397S,C420S,C422S,C430H No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.2；318 K；Ionic strength (raw mmCIF value) 150；Pressure ambient
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] CD4 coreceptor polypeptide, 200 mM [U-100% 2H] DPC, 150 mM sodium chloride, 20 mM sodium phosphate, 0.02 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2NXY HIV-1 gp120 Envelope Glycoprotein(S334A) Complexed with CD4 and Antibody 17b Deposited 2006-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 26–208（183 aa） Fragment：D1D2, N-TERMINAL TWO DOMAIN FRAGMENT
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 HEZ HEXANE-1,6-DIOL × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；7.0 % PEG 8000, 7.5 % 1,6-Hexanediol, 100 mM Na Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.231
2NXZ HIV-1 gp120 Envelope Glycoprotein (T257S, S334A, S375W) Complexed with CD4 and Antibody 17b Deposited 2006-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 26–208（183 aa） Fragment：D1D2, N-TERMINAL TWO DOMAIN FRAGMENT
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 EDO 1,2-ETHANEDIOL × 3 HEZ HEXANE-1,6-DIOL × 1 IPA ISOPROPYL ALCOHOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；7.5% PEG 4000, 8.5% MPD, 100 mM Na Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.04 Å R-free 0.244
2NY0 HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, T257S, V275C, S334A, S375W, A433M) Complexed with CD4 and Antibody 17b Deposited 2006-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 26–208（183 aa） Fragment：D1D2, N-TERMINAL TWO DOMAIN FRAGMENT
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 HEZ HEXANE-1,6-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；7.5% PEG 8000, 7.5% MPD, 100 mM Na Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.242
2NY1 HIV-1 gp120 Envelope Glycoprotein (I109C, T257S, S334A, S375W, Q428C) Complexed with CD4 and Antibody 17b Deposited 2006-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 26–208（183 aa） Fragment：D1D2, N-TERMINAL TWO DOMAIN FRAGMENT
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；7.5% PEG 8000, 7.5% MPD, 100 mM Na Citrate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.99 Å R-free 0.250
2NY2 HIV-1 gp120 Envelope Glycoprotein (T123C, T257S, S334A, S375W, G431C) Complexed with CD4 and Antibody 17b Deposited 2006-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 26–208（183 aa） Fragment：D1D2, N-TERMINAL TWO DOMAIN FRAGMENT
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11 EDO 1,2-ETHANEDIOL × 2 HEZ HEXANE-1,6-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；7.2% PEG 8000, 7.8% MPD, 100 mM Na Citrate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.223
2NY3 HIV-1 gp120 Envelope Glycoprotein (K231C, T257S, E267C, S334A, S375W) Complexed with CD4 and Antibody 17b Deposited 2006-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 26–208（183 aa） Fragment：D1D2, N-TERMINAL TWO DOMAIN FRAGMENT
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；8.5% PEG 4000, 8.5% MPD, 100 mM Na Citrate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.243
2NY4 HIV-1 gp120 Envelope Glycoprotein (K231C, T257S, E268C, S334A, S375W) Complexed with CD4 and Antibody 17b Deposited 2006-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 26–208（183 aa） Fragment：D1D2, N-TERMINAL TWO DOMAIN FRAGMENT
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 HEZ HEXANE-1,6-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；7.0% PEG 8000, 8.0% MPD, 100 mM Na Citrate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.241
2NY5 HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, I109C, T257S, V275C, S334A, S375W, Q428C, A433M) Complexed with CD4 and Antibody 17b Deposited 2006-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 26–208（183 aa） Fragment：D1D2, N-TERMINAL TWO DOMAIN FRAGMENT
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；9.2% PEG 4000, 9.5% MPD, 100 mM Na Citrate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.255
2NY6 HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, I109C, T123C, T257S, V275C,S334A, S375W, Q428C, G431C) Complexed with CD4 and Antibody 17b Deposited 2006-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 26–208（183 aa） Fragment：D1D2, N-TERMINAL TWO DOMAIN FRAGMENT
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；8.3% PEG 8000, 7.4% MPD, 100 mM Na Citrate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.276
2QAD Structure of tyrosine-sulfated 412d antibody complexed with HIV-1 YU2 gp120 and CD4 Deposited 2007-06-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 26–206（181 aa） Fragment：D1D2, IG-LIKE V-TYPE AND IG-LIKE C2-TYPE 1 DOMAINS
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 MLA MALONIC ACID × 2 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；17-19% polyethylene glycol (PEG) 1500, 0.1 M Na cacodylate pH 6.5, 0.2 M Na malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.30 Å R-free 0.269
2QAD Structure of tyrosine-sulfated 412d antibody complexed with HIV-1 YU2 gp120 and CD4 Deposited 2007-06-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 26–206（181 aa） Fragment：D1D2, IG-LIKE V-TYPE AND IG-LIKE C2-TYPE 1 DOMAINS
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 MLA MALONIC ACID × 2 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；17-19% polyethylene glycol (PEG) 1500, 0.1 M Na cacodylate pH 6.5, 0.2 M Na malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.30 Å R-free 0.269
2QAD Structure of tyrosine-sulfated 412d antibody complexed with HIV-1 YU2 gp120 and CD4 Deposited 2007-06-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 26–206（181 aa） Fragment：D1D2, IG-LIKE V-TYPE AND IG-LIKE C2-TYPE 1 DOMAINS
Chain F 26–206（181 aa） Fragment：D1D2, IG-LIKE V-TYPE AND IG-LIKE C2-TYPE 1 DOMAINS
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 MLA MALONIC ACID × 4 EDO 1,2-ETHANEDIOL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；17-19% polyethylene glycol (PEG) 1500, 0.1 M Na cacodylate pH 6.5, 0.2 M Na malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.30 Å R-free 0.269
3B71 CD4 endocytosis motif bound to the Focal Adhesion Targeting (FAT) domain of the Focal Adhesion Kinase Deposited 2007-10-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 428–450（23 aa） Fragment：residues 403-425
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；3.9 M NaCl, 2.5 % glycerol, 100 mM Hepes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.82 Å R-free 0.307
3B71 CD4 endocytosis motif bound to the Focal Adhesion Targeting (FAT) domain of the Focal Adhesion Kinase Deposited 2007-10-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 428–450（23 aa） Fragment：residues 403-425
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；3.9 M NaCl, 2.5 % glycerol, 100 mM Hepes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.82 Å R-free 0.307
3B71 CD4 endocytosis motif bound to the Focal Adhesion Targeting (FAT) domain of the Focal Adhesion Kinase Deposited 2007-10-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 428–450（23 aa） Fragment：residues 403-425
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；3.9 M NaCl, 2.5 % glycerol, 100 mM Hepes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.82 Å R-free 0.307
3CD4 REFINEMENT AND ANALYSIS OF THE FIRST TWO DOMAINS OF HUMAN CD4 Deposited 1992-07-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 26–207（182 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å
3J70 Model of gp120, including variable regions, in complex with CD4 and 17b Deposited 2014-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain C 26–208（183 aa） Fragment：UNP residues 26-208
Chain O 26–208（183 aa） Fragment：UNP residues 26-208
Chain T 26–208（183 aa） Fragment：UNP residues 26-208
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 20.00 Å
3JCB Structure of Simian Immunodeficiency Virus Envelope Spikes bound with CD4 and Monoclonal Antibody 36D5 Deposited 2015-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 26–200（175 aa） Fragment：UNP residues 26-200
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane.
Resolution not provided
3JCC Structure of Simian Immunodeficiency Virus Envelope Spikes bound with CD4 and Monoclonal Antibody 36D5 Deposited 2015-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 26–200（175 aa） Fragment：UNP residues 26-200
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane.
Resolution not provided
3JWD Structure of HIV-1 gp120 with gp41-Interactive Region: Layered Architecture and Basis of Conformational Mobility Deposited 2009-09-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 26–208（183 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9.5；293 K；4.5 % PEG 8000, 01M CHES, pH 9.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.61 Å R-free 0.275
3JWD Structure of HIV-1 gp120 with gp41-Interactive Region: Layered Architecture and Basis of Conformational Mobility Deposited 2009-09-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 26–208（183 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9.5；293 K；4.5 % PEG 8000, 01M CHES, pH 9.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.61 Å R-free 0.275
3JWO Structure of HIV-1 gp120 with gp41-Interactive Region: Layered Architecture and Basis of Conformational Mobility Deposited 2009-09-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 26–208（183 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；5.3% PEG8000, 0.2M Calcium acetate, 0.1M imidazole, pH 8.0, VAPOR DIFFUSION, temperature 293K
Resolution 3.51 Å R-free 0.273
3LQA Crystal structure of clade C gp120 in complex with sCD4 and 21c Fab Deposited 2010-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 26–207（182 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；20% (w/v) PEG monomethyl ether 2000, 5% (v/v) PEG 200, 0.2 M Trimethylamine N-oxide, 0.1 M Tris-HCl pH 8.5 , VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.40 Å R-free 0.322
3O2D Crystal structure of HIV-1 primary receptor CD4 in complex with a potent antiviral antibody Deposited 2010-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 26–207（182 aa） Fragment：UNP residues 26-207
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；3 M Na malonate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.19 Å R-free 0.224
3S4S Crystal structure of CD4 mutant bound to HLA-DR1 Deposited 2011-05-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 26–203（178 aa） Fragment：UNP residues 26-203
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；PEG 8000, (NH4)SO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.286
3S4S Crystal structure of CD4 mutant bound to HLA-DR1 Deposited 2011-05-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 26–203（178 aa） Fragment：UNP residues 26-203
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；PEG 8000, (NH4)SO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.286
3S5L Crystal structure of CD4 mutant bound to HLA-DR1 Deposited 2011-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 26–203（178 aa） Fragment：CD4
Mutation：Q40Y, T45W, S60R, D63R GOL GLYCEROL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；PEG 8000, (NH4)SO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.10 Å R-free 0.268
3S5L Crystal structure of CD4 mutant bound to HLA-DR1 Deposited 2011-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 26–203（178 aa） Fragment：CD4
Mutation：Q40Y, T45W, S60R, D63R GOL GLYCEROL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；PEG 8000, (NH4)SO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.10 Å R-free 0.268
3T0E Crystal structure of a complete ternary complex of T cell receptor, peptide-MHC and CD4 Deposited 2011-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 26–388（363 aa） Fragment：unp residues 26-398
Mutation：Q40Y, T45W No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8；277 K；10 mM Tris-HCl pH8, 10 mM NaAc pH5.2, 5 mM NaCl, EVAPORATION, temperature 277K
Resolution 4.00 Å R-free 0.305
4H8W Crystal structure of non-neutralizing and ADCC-potent antibody N5-i5 in complex with HIV-1 clade A/E gp120 and sCD4. Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 26–208（183 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；11-13% PEG 8000, 100 mM Tris-HCl pH 8.5, 65 mM sodium chloride added to well after mixing drop, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.85 Å R-free 0.215
4JM2 Crystal Structure of PGT 135 Fab in Complex with gp120 Core Protein from HIV-1 Strain JR-FL Bound to CD4 and 17b Fab Deposited 2013-03-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric
Chain F 26–208（183 aa） Fragment：Ig-like V-type and C2-type 1 domains (UNP residues 26-208)
Not recorded PG4 TETRAETHYLENE GLYCOL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20% PEG2000, 0.1 M Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.10 Å R-free 0.285
4Q6I Crystal structure of murine 2D5 Fab, a potent anti-CD4 HIV-1-neutralizing antibody in complex with CD4 Deposited 2014-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 1–208（208 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；1.5 M (NH4)2SO4, 200 mM MgCl2, 150 mM NaCl, 100 mM NaAc pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.65 Å R-free 0.257
4Q6I Crystal structure of murine 2D5 Fab, a potent anti-CD4 HIV-1-neutralizing antibody in complex with CD4 Deposited 2014-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–208（208 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；1.5 M (NH4)2SO4, 200 mM MgCl2, 150 mM NaCl, 100 mM NaAc pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.65 Å R-free 0.257
4Q6I Crystal structure of murine 2D5 Fab, a potent anti-CD4 HIV-1-neutralizing antibody in complex with CD4 Deposited 2014-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–208（208 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；1.5 M (NH4)2SO4, 200 mM MgCl2, 150 mM NaCl, 100 mM NaAc pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.65 Å R-free 0.257
4Q6I Crystal structure of murine 2D5 Fab, a potent anti-CD4 HIV-1-neutralizing antibody in complex with CD4 Deposited 2014-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–208（208 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；1.5 M (NH4)2SO4, 200 mM MgCl2, 150 mM NaCl, 100 mM NaAc pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.65 Å R-free 0.257
4R2G Crystal Structure of PGT124 Fab bound to HIV-1 JRCSF gp120 core and to CD4 Deposited 2014-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 26–208（183 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CL CHLORIDE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；2.4M ammonium sulphate, 0.1M Tris, 13% glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.28 Å R-free 0.263
4R2G Crystal Structure of PGT124 Fab bound to HIV-1 JRCSF gp120 core and to CD4 Deposited 2014-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 26–208（183 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 CL CHLORIDE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；2.4M ammonium sulphate, 0.1M Tris, 13% glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.28 Å R-free 0.263
4R2G Crystal Structure of PGT124 Fab bound to HIV-1 JRCSF gp120 core and to CD4 Deposited 2014-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 26–208（183 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CL CHLORIDE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；2.4M ammonium sulphate, 0.1M Tris, 13% glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.28 Å R-free 0.263
4R2G Crystal Structure of PGT124 Fab bound to HIV-1 JRCSF gp120 core and to CD4 Deposited 2014-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain L 26–208（183 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CL CHLORIDE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；2.4M ammonium sulphate, 0.1M Tris, 13% glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.28 Å R-free 0.263
4R4H Crystal structure of non-neutralizing, A32-like antibody 2.2c in complex with HIV-1 Env gp120 Deposited 2014-08-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 26–203（178 aa） Fragment：UNP residues 26-203
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；10% PEG 5000 MME, 100 mM sodium acetate, and 100 mM Tris-HCl pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 4.28 Å R-free 0.320
4RQS Crystal structure of fully glycosylated HIV-1 gp120 core bound to CD4 and 17b Fab Deposited 2014-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 26–208（183 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；1.4 M sodium formate, 16.6% PEG 3350, 0.1 M CaCl2, 0.1 M Acetate pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 4.49 Å R-free 0.322
4RQS Crystal structure of fully glycosylated HIV-1 gp120 core bound to CD4 and 17b Fab Deposited 2014-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 26–208（183 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；1.4 M sodium formate, 16.6% PEG 3350, 0.1 M CaCl2, 0.1 M Acetate pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 4.49 Å R-free 0.322
5A7X negative stain EM of BG505 SOSIP.664 in complex with sCD4, 17b, and 8ANC195 Deposited 2015-07-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain B 26–206（181 aa）
Chain F 26–206（181 aa）
Chain J 26–206（181 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 ELECTRON MICROSCOPY
cryo-EM buffer 20MM TRIS, 50 MM NACL；pH 8；20MM TRIS, 50 MM NACL
Resolution 17.00 Å
5A8H cryo-ET subtomogram averaging of BG505 SOSIP.664 in complex with sCD4, 17b, and 8ANC195 Deposited 2015-07-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain B 26–208（183 aa） Fragment：SOLUBLE CD4 D1-D2 DOMAINS, RESIDUES26-208
Chain H 26–208（183 aa） Fragment：SOLUBLE CD4 D1-D2 DOMAINS, RESIDUES26-208
Chain N 26–208（183 aa） Fragment：SOLUBLE CD4 D1-D2 DOMAINS, RESIDUES26-208
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 ELECTRON MICROSCOPY
cryo-EM buffer 20MM TRIS, 50MM NACL；pH 8；20MM TRIS, 50MM NACL
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, HUMIDITY- 95, TEMPERATURE- 70, INSTRUMENT- FEI
Resolution 23.00 Å
5CAY Envelope glycoprotein gp120 core from HIV type 2 bound to the first two domains of human soluble CD4 receptor Deposited 2015-06-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 26–208（183 aa） Fragment：domains 1 and 2 (UNP residues 26-208)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.15M DL-Malic acid 7.0, 0.1M imidazole pH 7.0, 22% PEGMME 550
Resolution 3.00 Å R-free 0.287
5THR Cryo-EM structure of a BG505 Env-sCD4-17b-8ANC195 complex Deposited 2016-09-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 21-meric
Chain G 26–207（182 aa） Fragment：UNP residues 26-207
Chain H 26–207（182 aa） Fragment：UNP residues 26-207
Chain I 26–207（182 aa） Fragment：UNP residues 26-207
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 8.90 Å
5U1F Initial contact of HIV-1 Env with CD4: Cryo-EM structure of BG505 DS-SOSIP trimer in complex with CD4 and antibody PGT145 Deposited 2016-11-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain M 26–388（363 aa） Fragment：UNP residues 26-388
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.80 Å
5VN3 Cryo-EM model of B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen binding variable domain of 17b Deposited 2017-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain C 26–208（183 aa）
Chain E 26–208（183 aa）
Chain F 26–208（183 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；DDM was added to a final concentration of 0.06 mM prior to vitrification
cryo-EM vitrification conditions Cryogen ETHANE；3 uL of sample applied to a holey carbon grid on glow discharged face and blotted manually on sample side until filter paper detached from grid, followed by immediate plunging
Resolution 3.70 Å
6CM3 BG505 SOSIP in complex with sCD4, 17b, 8ANC195 Deposited 2018-03-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 21-meric
Chain G 26–207（182 aa）
Chain H 26–207（182 aa）
Chain I 26–207（182 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.54 Å
6EDU B41 SOSIP.664 in complex with soluble CD4 (D1-D2), the co-receptor mimicking antibody 21c and the broadly neutralizing antibody 8ANC195 Deposited 2018-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 21-meric
Chain G 26–208（183 aa）
Chain H 26–208（183 aa）
Chain I 26–208（183 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.06 Å
6L1Y structure of gp120/CD4 with a non-canonical surface Deposited 2019-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 26–202（177 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7.4；293 K；0.1 M HEPES sodium, pH 7.4, 11% PEG 4000 and 10% 2-propanol
Resolution 2.47 Å R-free 0.257
6MEO Structural basis of coreceptor recognition by HIV-1 envelope spike Deposited 2018-09-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 26–201（176 aa） Fragment：Ig-like V-type and Ig-like C2-type 1 domains, residues 26-201
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 BMA beta-D-mannopyranose × 1 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；100 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, 0.001% LMNG (w/v), 0.025% DDM (w/v), and 0.04 % CHS (w/v)
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6MET Structural basis of coreceptor recognition by HIV-1 envelope spike Deposited 2018-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 26–388（363 aa） Fragment：Ig-like V-type 1 and Ig-like C2-type 1,2,3 domains, residues 26-388
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；100 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, 0.001% LMNG (w/v), 0.025% DDM (w/v), and 0.04 % CHS (w/v).
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6OPN CD4- and 17-bound HIV-1 Env B41 SOSIP in complex with small molecule GO35 Deposited 2019-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric
Chain C 25–203（179 aa）
Chain F 25–203（179 aa）
Chain I 25–203（179 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 N07 [3'-(5-methyl-1,3,4-oxadiazol-2-yl)[1,1'-biphenyl]-3-yl](piperidin-1-yl)methanone × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Detergent (LMNG) added shortly (<5 minutes) prior to grid freezing using an 8X concentrated stock.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6OPO Symmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with DDM Deposited 2019-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain C 25–203（179 aa）
Chain G 25–203（179 aa）
Chain N 25–203（179 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 LMT DODECYL-BETA-D-MALTOSIDE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；DDM added shortly (<5 minutes) prior to freezing.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6OPP Asymmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with DDM Deposited 2019-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain C 25–203（179 aa）
Chain F 25–203（179 aa）
Chain M 25–203（179 aa）
Not recorded LMT DODECYL-BETA-D-MALTOSIDE × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Detergent added shortly (<5 minutes) prior to grid freezing
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6OPQ CD4- and 17-bound HIV-1 Env B41 SOSIP frozen with LMNG Deposited 2019-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain C 25–203（179 aa）
Chain I 25–203（179 aa）
Chain J 25–203（179 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Detergent (LMNG) added shortly (<5 minutes) prior to grid freezing using an 8X concentrated stock.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6U0L Asymmetrically open conformational state (Class I) of HIV-1 Env trimer BG505 SOSIP.664 in complex with sCD4 and E51 Fab Deposited 2019-08-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain D 26–207（182 aa） Fragment：D1-D2 domain
Chain E 26–207（182 aa） Fragment：D1-D2 domain
Chain F 26–207（182 aa） Fragment：D1-D2 domain
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6U0N Asymmetrically open conformational state (Class II) of HIV-1 Env trimer BG505 SOSIP.664 in complex with sCD4 and E51 Fab Deposited 2019-08-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain D 26–207（182 aa）
Chain E 26–207（182 aa）
Chain F 26–207（182 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6X5B Symmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with small molecule GO52 Deposited 2020-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain C 25–203（179 aa）
Chain G 25–203（179 aa）
Chain N 25–203（179 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 UOV N-(4'-methyl[1,1'-biphenyl]-4-yl)-1-oxa-7-azaspiro[3.5]nonane-7-carboxamide × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Detergent diluted into sample shortly before application to grid
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6X5C Asymmetric model of CD4-bound B41 HIV-1 Env SOSIP in complex with small molecule GO52 Deposited 2020-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric
Chain C 25–203（179 aa）
Chain I 25–203（179 aa）
Chain J 25–203（179 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23 UOV N-(4'-methyl[1,1'-biphenyl]-4-yl)-1-oxa-7-azaspiro[3.5]nonane-7-carboxamide × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Detergent diluted into sample shortly before application to grid
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.04 Å
7T0O cryoEM reconstruction of the HIV gp140 in complex with the extracellular domains of CD4 and the adnectin domain of Combinectin. The gp140 and CD4 coordinates from entry 6EDU were rigid body fitted to the EM map along withe the crystal structure of CD4+adnectin Deposited 2021-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain H 26–389（364 aa）
Chain L 26–389（364 aa）
Chain M 26–389（364 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
7T0R Crystal structure of the anti-CD4 adnectin 6940_B01 as a complex with the extracellular domains of CD4 and ibalizumab fAb Deposited 2021-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 26–389（364 aa） Fragment：Extra-cellular domains D1-D4
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.01 M Na3 Citrate, 15.5% PEG3350, 0.3 M (NH4)2H Citrate, 0.1 M AmSO4
Resolution 3.65 Å R-free 0.292
7T0R Crystal structure of the anti-CD4 adnectin 6940_B01 as a complex with the extracellular domains of CD4 and ibalizumab fAb Deposited 2021-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 26–389（364 aa） Fragment：Extra-cellular domains D1-D4
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.01 M Na3 Citrate, 15.5% PEG3350, 0.3 M (NH4)2H Citrate, 0.1 M AmSO4
Resolution 3.65 Å R-free 0.292
7TXD Cryo-EM structure of BG505 SOSIP HIV-1 Env trimer in complex with CD4 receptor (D1D2) and broadly neutralizing darpin bnD.9 Deposited 2022-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 26–208（183 aa） Fragment：D1-D2
Chain H 26–208（183 aa） Fragment：D1-D2
Chain I 26–208（183 aa） Fragment：D1-D2
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.87 Å
8D5C anti-HIV-1 gp120-sCD4 complex antibody CG10 Fab in complex with B41-sCD4 Deposited 2022-06-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain D 26–208（183 aa）
Chain E 26–208（183 aa）
Chain F 26–208（183 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8FYI Structure of HIV-1 BG505 SOSIP-HT1 in complex with one CD4 molecule Deposited 2023-01-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric
Chain Z 26–396（371 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8FYJ Structure of HIV-1 BG505 SOSIP-HT2 in complex with two CD4 molecules (class I) Deposited 2023-01-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric
Chain Y 26–396（371 aa）
Chain Z 26–396（371 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8W90 crystal structure of CD4-D1D2 with Nb457 Deposited 2023-09-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 26–203（178 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；0.1 M sodium cacodylate trihydrate pH 6.8, 1.4 M sodium acetate trihydrate
Resolution 1.81 Å R-free 0.206
8W90 crystal structure of CD4-D1D2 with Nb457 Deposited 2023-09-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 26–203（178 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；0.1 M sodium cacodylate trihydrate pH 6.8, 1.4 M sodium acetate trihydrate
Resolution 1.81 Å R-free 0.206
8W90 crystal structure of CD4-D1D2 with Nb457 Deposited 2023-09-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 26–203（178 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；0.1 M sodium cacodylate trihydrate pH 6.8, 1.4 M sodium acetate trihydrate
Resolution 1.81 Å R-free 0.206
8Z7N Structure of HIV-1 CH119 SOSIP.664 trimer in complex with CD4 molecules Deposited 2024-04-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain C 1–392（392 aa）
Chain F 1–392（392 aa）
Chain I 1–392（392 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.58 Å
9D8Y Cryo-EM structure of HIV-1 BG505 SOSIP.664 Env bound to 3-sCD4, 3-VRC34.01 Fab with one gp120 rotated, Population 4 Deposited 2024-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain M 26–121（96 aa） Fragment：residues 1-96
Chain N 26–121（96 aa） Fragment：residues 1-96
Chain O 26–121（96 aa） Fragment：residues 1-96
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.06 Å
9D90 Cryo-EM structure of partially open HIV-1 BG505 SOSIP.664 Env bound to 3-sCD4, 3-17b Fab and 3-VRC34.01 Fab, Population 1 Deposited 2024-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 21-meric
Chain M 26–206（181 aa）
Chain N 26–206（181 aa）
Chain O 26–206（181 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.91 Å
9D98 Cryo-EM structure of HIV-1 BG505 SOSIP.664 Env bound to 3-sCD4, 3-VRC34.01 Fab with two gp120 protomers rotated, Population 5 Deposited 2024-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain M 26–206（181 aa）
Chain N 26–206（181 aa）
Chain O 26–206（181 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.19 Å
9MET CXCR4-HIV-2/gp120-CD4 Deposited 2024-12-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 26–201（176 aa） Fragment：Ig-like V-type and Ig-like C2-type 1 domains (UNP residues 26-201)
Chain R 26–201（176 aa） Fragment：Ig-like V-type and Ig-like C2-type 1 domains (UNP residues 26-201)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.65 Å
9OAJ AMC008 v4.2 SOSIP Env trimer in complex with CD4 D1D2 Deposited 2025-04-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric
Chain C 1–458（458 aa）
Chain D 1–458（458 aa）
Chain G 1–458（458 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å

78 other PDB entries and 99 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CD4_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain C； PDBConstruct 1–182； UniProt 26–207

Envelope glycoprotein gp160

Human immunodeficiency virus 1

UniProt Q0ED31

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 4 其他Polymer 6 PDB declaration: tetrameric（4） Consistent with protein copy count Chain G； UniProt 43–122 Fragment：GP120 CORE, (UNP RESIDUES 43-122, 201-303, 325-486) T-cell surface glycoprotein CD4 × 1 （P01730） Fab heavy chain × 1 Fab light chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 BEN BENZAMIDINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.3；298 K；PEG 3350, HEPES, benzamidine Resolution 3.00 Å R-free 0.272

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4P9H Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3NGB Crystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 gp120 Deposited 2010-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 43–122（80 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain G 201–303（103 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain G 325–486（162 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11 BGC beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；10% PEG 4000, 9% Isopropanol, 0.1M Ammonium Sulfate, 0.1M Tris/Cl-, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.68 Å R-free 0.256
3NGB Crystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 gp120 Deposited 2010-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 43–122（80 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain A 201–303（103 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain A 325–486（162 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 BGC beta-D-glucopyranose × 7 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；10% PEG 4000, 9% Isopropanol, 0.1M Ammonium Sulfate, 0.1M Tris/Cl-, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.68 Å R-free 0.256
3NGB Crystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 gp120 Deposited 2010-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 43–122（80 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain D 201–303（103 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain D 325–486（162 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 BGC beta-D-glucopyranose × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；10% PEG 4000, 9% Isopropanol, 0.1M Ammonium Sulfate, 0.1M Tris/Cl-, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.68 Å R-free 0.256
3NGB Crystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 gp120 Deposited 2010-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 43–122（80 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain I 201–303（103 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain I 325–486（162 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11 BGC beta-D-glucopyranose × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；10% PEG 4000, 9% Isopropanol, 0.1M Ammonium Sulfate, 0.1M Tris/Cl-, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.68 Å R-free 0.256
3U7Y Structure of NIH45-46 Fab in complex with gp120 of 93TH057 HIV Deposited 2011-10-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 43–122（80 aa） Fragment：gp120 core (UNP RESIDUES 43-122, 201-303, 325-486)
Chain G 201–303（103 aa） Fragment：gp120 core (UNP RESIDUES 43-122, 201-303, 325-486)
Chain G 325–486（162 aa） Fragment：gp120 core (UNP RESIDUES 43-122, 201-303, 325-486)
Mutation：V65C, S115C Mutation：V65C, S115C Mutation：V65C, S115C FLC CITRATE ANION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；12% isopropanol, 10% polyethylene glycol 10,000, 0.1 M sodium citrate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.45 Å R-free 0.256
4DKU Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-09027 Deposited 2012-02-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–122（80 aa） Fragment：Chimera residue 44-492
Chain A 201–303（103 aa） Fragment：Chimera residue 44-492
Chain A 325–486（162 aa） Fragment：Chimera residue 44-492
Mutation：V1V2 and V3 deletion, H375S Mutation：V1V2 and V3 deletion, H375S Mutation：V1V2 and V3 deletion, H375S NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 0KU N-(4-chlorophenyl)-N'-{(S)-[5-(hydroxymethyl)-4-methyl-1,3-thiazol-2-yl][(2S)-piperidin-2-yl]methyl}ethanediamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；10% PEG 8000, 5% iso-propanol, 0.1M HEPES 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.49 Å R-free 0.249
4DKU Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-09027 Deposited 2012-02-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–122（80 aa） Fragment：Chimera residue 44-492
Chain B 201–303（103 aa） Fragment：Chimera residue 44-492
Chain B 325–486（162 aa） Fragment：Chimera residue 44-492
Mutation：V1V2 and V3 deletion, H375S Mutation：V1V2 and V3 deletion, H375S Mutation：V1V2 and V3 deletion, H375S NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 0KU N-(4-chlorophenyl)-N'-{(S)-[5-(hydroxymethyl)-4-methyl-1,3-thiazol-2-yl][(2S)-piperidin-2-yl]methyl}ethanediamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；10% PEG 8000, 5% iso-propanol, 0.1M HEPES 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.49 Å R-free 0.249
4DKV Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-10007 Deposited 2012-02-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–122（80 aa） Fragment：Chimera residues 44-492
Chain A 201–303（103 aa） Fragment：Chimera residues 44-492
Chain A 325–486（162 aa） Fragment：Chimera residues 44-492
Mutation：V1V2 and V3 deletion, His 375 to Ser Mutation：V1V2 and V3 deletion, His 375 to Ser Mutation：V1V2 and V3 deletion, His 375 to Ser NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 0KW N-(4-chlorophenyl)-N'-{(S)-[5-(2-hydroxyethyl)-4-methyl-1,3-thiazol-2-yl][(2S)-piperidin-2-yl]methyl}ethanediamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；10% PEG 8000, 5% iso-propanol, 0.1M HEPES 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.18 Å R-free 0.235
4DKV Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-10007 Deposited 2012-02-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–122（80 aa） Fragment：Chimera residues 44-492
Chain B 201–303（103 aa） Fragment：Chimera residues 44-492
Chain B 325–486（162 aa） Fragment：Chimera residues 44-492
Mutation：V1V2 and V3 deletion, His 375 to Ser Mutation：V1V2 and V3 deletion, His 375 to Ser Mutation：V1V2 and V3 deletion, His 375 to Ser NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 0KW N-(4-chlorophenyl)-N'-{(S)-[5-(2-hydroxyethyl)-4-methyl-1,3-thiazol-2-yl][(2S)-piperidin-2-yl]methyl}ethanediamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；10% PEG 8000, 5% iso-propanol, 0.1M HEPES 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.18 Å R-free 0.235
4OLU Crystal structure of antibody VRC07 in complex with clade A/E 93TH057 HIV-1 gp120 core Deposited 2014-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 43–122（80 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain G 201–303（103 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain G 325–486（162 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；12% PEG 4000, 0.2M Sodium Acetate, 0.1M Tris 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.248
4OLV Crystal structure of antibody VRC07-G54F in complex with clade A/E 93TH057 HIV-1 gp120 core Deposited 2014-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 43–122（80 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain G 201–303（103 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain G 325–486（162 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；12% PEG 4000, 0.2M Sodium Acetate, 0.1M Tris 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.253
4OLW Crystal structure of antibody VRC07-G54H in complex with clade A/E 93TH057 HIV-1 gp120 core Deposited 2014-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 43–122（80 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain G 201–303（103 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain G 325–486（162 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；10% PEG 4000, 0.2M Sodium Acetate, 0.1M Tris 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.71 Å R-free 0.257
4OLX Crystal structure of antibody VRC07-G54L in complex with clade A/E 93TH057 HIV-1 gp120 core Deposited 2014-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 43–122（80 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain G 201–303（103 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain G 325–486（162 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；12% PEG 4000, 0.2M Sodium Acetate, 0.1M Tris 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.247
4OLY Crystal structure of antibody VRC07-G54R in complex with clade A/E 93TH057 HIV-1 gp120 core Deposited 2014-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 43–122（80 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain G 201–303（103 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain G 325–486（162 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；12% PEG 4000, 0.2M Sodium Acetate, 0.1M Tris 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.35 Å R-free 0.244
4OLZ Crystal structure of antibody VRC07-G54W in complex with clade A/E 93TH057 HIV-1 gp120 core Deposited 2014-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 43–122（80 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain G 201–303（103 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain G 325–486（162 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；14% PEG 4000, 0.2M Sodium Acetate, 0.1M Tris 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.254
4OM0 Crystal structure of antibody VRC07-G54Y in complex with clade A/E 93TH057 HIV-1 gp120 core Deposited 2014-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 43–122（80 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain G 201–303（103 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain G 325–486（162 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；14% PEG 4000, 0.2M Sodium Acetate, 0.1M Tris 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.29 Å R-free 0.247
4OM1 Crystal structure of antibody VRC07-I30Q, G54W, S58N in complex with clade A/E 93TH057 HIV-1 gp120 core Deposited 2014-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 43–122（80 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain G 201–303（103 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain G 325–486（162 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；14% PEG 4000, 0.2M Sodium Acetate, 0.1M Tris 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.13 Å R-free 0.226
4RZ8 Crystal structure of HIV-1 gp120 core in complex with NBD-11021, a small molecule CD4-antagonist Deposited 2014-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–122（80 aa） Fragment：UNP residues 43-122, 201-303, 325-486
Chain A 201–303（103 aa） Fragment：UNP residues 43-122, 201-303, 325-486
Chain A 325–486（162 aa） Fragment：UNP residues 43-122, 201-303, 325-486
Mutation：V1V2 and V3 deletion, H375S Mutation：V1V2 and V3 deletion, H375S Mutation：V1V2 and V3 deletion, H375S NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 3ZM 5-(4-chlorophenyl)-N-{(S)-[5-(hydroxymethyl)-4-methyl-1,3-thiazol-2-yl][(2R)-piperidin-2-yl]methyl}-1H-pyrrole-2-carboxamide × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；10% PEG 8000, 5% iso-propanol, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.90 Å R-free 0.243
4RZ8 Crystal structure of HIV-1 gp120 core in complex with NBD-11021, a small molecule CD4-antagonist Deposited 2014-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–122（80 aa） Fragment：UNP residues 43-122, 201-303, 325-486
Chain B 201–303（103 aa） Fragment：UNP residues 43-122, 201-303, 325-486
Chain B 325–486（162 aa） Fragment：UNP residues 43-122, 201-303, 325-486
Mutation：V1V2 and V3 deletion, H375S Mutation：V1V2 and V3 deletion, H375S Mutation：V1V2 and V3 deletion, H375S NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 3ZM 5-(4-chlorophenyl)-N-{(S)-[5-(hydroxymethyl)-4-methyl-1,3-thiazol-2-yl][(2R)-piperidin-2-yl]methyl}-1H-pyrrole-2-carboxamide × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；10% PEG 8000, 5% iso-propanol, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.90 Å R-free 0.243
4RZ8 Crystal structure of HIV-1 gp120 core in complex with NBD-11021, a small molecule CD4-antagonist Deposited 2014-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 43–122（80 aa） Fragment：UNP residues 43-122, 201-303, 325-486
Chain C 201–303（103 aa） Fragment：UNP residues 43-122, 201-303, 325-486
Chain C 325–486（162 aa） Fragment：UNP residues 43-122, 201-303, 325-486
Mutation：V1V2 and V3 deletion, H375S Mutation：V1V2 and V3 deletion, H375S Mutation：V1V2 and V3 deletion, H375S NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11 3ZM 5-(4-chlorophenyl)-N-{(S)-[5-(hydroxymethyl)-4-methyl-1,3-thiazol-2-yl][(2R)-piperidin-2-yl]methyl}-1H-pyrrole-2-carboxamide × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；10% PEG 8000, 5% iso-propanol, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.90 Å R-free 0.243
4RZ8 Crystal structure of HIV-1 gp120 core in complex with NBD-11021, a small molecule CD4-antagonist Deposited 2014-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 43–122（80 aa） Fragment：UNP residues 43-122, 201-303, 325-486
Chain D 201–303（103 aa） Fragment：UNP residues 43-122, 201-303, 325-486
Chain D 325–486（162 aa） Fragment：UNP residues 43-122, 201-303, 325-486
Mutation：V1V2 and V3 deletion, H375S Mutation：V1V2 and V3 deletion, H375S Mutation：V1V2 and V3 deletion, H375S NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11 3ZM 5-(4-chlorophenyl)-N-{(S)-[5-(hydroxymethyl)-4-methyl-1,3-thiazol-2-yl][(2R)-piperidin-2-yl]methyl}-1H-pyrrole-2-carboxamide × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；10% PEG 8000, 5% iso-propanol, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.90 Å R-free 0.243
4XNZ Crystal structure of broadly and potently neutralizing antibody VRC06B in complex with HIV-1 clade A/E strain 93TH057 gp120 Deposited 2015-01-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 43–122（80 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain G 201–303（103 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain G 325–486（162 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；7% PEG 3350, 2.5% isopropanol, 0.1M Tris-HCl, pH 8.5
Resolution 3.39 Å R-free 0.301
4XNZ Crystal structure of broadly and potently neutralizing antibody VRC06B in complex with HIV-1 clade A/E strain 93TH057 gp120 Deposited 2015-01-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 43–122（80 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain A 201–303（103 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain A 325–486（162 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；7% PEG 3350, 2.5% isopropanol, 0.1M Tris-HCl, pH 8.5
Resolution 3.39 Å R-free 0.301
4XNZ Crystal structure of broadly and potently neutralizing antibody VRC06B in complex with HIV-1 clade A/E strain 93TH057 gp120 Deposited 2015-01-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 43–122（80 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain D 201–303（103 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Chain D 325–486（162 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；7% PEG 3350, 2.5% isopropanol, 0.1M Tris-HCl, pH 8.5
Resolution 3.39 Å R-free 0.301
4YDJ Crystal structure of broadly and potently neutralizing antibody 44-VRC13.01 in complex with HIV-1 clade AE strain 93TH057 gp120 Deposited 2015-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 43–122（80 aa） Fragment：UNP residues 43-122, 201-303, 325-486
Chain G 201–303（103 aa） Fragment：UNP residues 43-122, 201-303, 325-486
Chain G 325–486（162 aa） Fragment：UNP residues 43-122, 201-303, 325-486
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11 IPA ISOPROPYL ALCOHOL × 2 BU3 (R,R)-2,3-BUTANEDIOL × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；9.5% PEG 8000, 15% isopropanol, 0.1M imidazole, pH 6.5
Resolution 2.31 Å R-free 0.249
4YDJ Crystal structure of broadly and potently neutralizing antibody 44-VRC13.01 in complex with HIV-1 clade AE strain 93TH057 gp120 Deposited 2015-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 43–122（80 aa） Fragment：UNP residues 43-122, 201-303, 325-486
Chain I 201–303（103 aa） Fragment：UNP residues 43-122, 201-303, 325-486
Chain I 325–486（162 aa） Fragment：UNP residues 43-122, 201-303, 325-486
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11 IPA ISOPROPYL ALCOHOL × 1 BU3 (R,R)-2,3-BUTANEDIOL × 3 PEG DI(HYDROXYETHYL)ETHER × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；9.5% PEG 8000, 15% isopropanol, 0.1M imidazole, pH 6.5
Resolution 2.31 Å R-free 0.249
4YDK Crystal structure of broadly and potently neutralizing antibody C38-VRC16.01 in complex with HIV-1 clade AE strain 93TH057 gp120 Deposited 2015-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 43–122（80 aa） Fragment：UNP residues 43-122, 201-303, 325-486,UNP residues 43-122, 201-303, 325-486,UNP residues 43-122, 201-303, 325-486
Chain G 201–303（103 aa） Fragment：UNP residues 43-122, 201-303, 325-486,UNP residues 43-122, 201-303, 325-486,UNP residues 43-122, 201-303, 325-486
Chain G 325–486（162 aa） Fragment：UNP residues 43-122, 201-303, 325-486,UNP residues 43-122, 201-303, 325-486,UNP residues 43-122, 201-303, 325-486
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 PEG DI(HYDROXYETHYL)ETHER × 7 GOL GLYCEROL × 13 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；293 K；7.5% PEG 8000, 0.1M CHES, pH 9.5
Resolution 2.05 Å R-free 0.206
4YDL Crystal structure of broadly and potently neutralizing antibody C38-VRC18.02 in complex with HIV-1 clade AE strain 93TH057gp120 Deposited 2015-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 43–122（80 aa） Fragment：UNP residues 43-122, 201-303, 325-486
Chain G 201–303（103 aa） Fragment：UNP residues 43-122, 201-303, 325-486
Chain G 325–486（162 aa） Fragment：UNP residues 43-122, 201-303, 325-486
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；9.0% PEG 4000, 4.5% isopropanol, 0.1M HEPES, pH 7.5
Resolution 1.80 Å R-free 0.207
4YDL Crystal structure of broadly and potently neutralizing antibody C38-VRC18.02 in complex with HIV-1 clade AE strain 93TH057gp120 Deposited 2015-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 43–122（80 aa） Fragment：UNP residues 43-122, 201-303, 325-486
Chain A 201–303（103 aa） Fragment：UNP residues 43-122, 201-303, 325-486
Chain A 325–486（162 aa） Fragment：UNP residues 43-122, 201-303, 325-486
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；9.0% PEG 4000, 4.5% isopropanol, 0.1M HEPES, pH 7.5
Resolution 1.80 Å R-free 0.207
4YFL Crystal structure of VH1-46 germline-derived CD4-binding site-directed antibody 1B2530 in complex with HIV-1 clade A/E 93TH057 gp120 Deposited 2015-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 43–122（80 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486,UNP RESIDUES 43-122, 201-303, 325-486,UNP RESIDUES 43-122, 201-303, 325-486
Chain G 201–303（103 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486,UNP RESIDUES 43-122, 201-303, 325-486,UNP RESIDUES 43-122, 201-303, 325-486
Chain G 325–486（162 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486,UNP RESIDUES 43-122, 201-303, 325-486,UNP RESIDUES 43-122, 201-303, 325-486
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；8% w/v PEG 8000, 0.2 M sodium acetate and 0.1 m sodium cacodylate, pH 6.5
Resolution 3.39 Å R-free 0.326
4YFL Crystal structure of VH1-46 germline-derived CD4-binding site-directed antibody 1B2530 in complex with HIV-1 clade A/E 93TH057 gp120 Deposited 2015-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 43–122（80 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486,UNP RESIDUES 43-122, 201-303, 325-486,UNP RESIDUES 43-122, 201-303, 325-486
Chain E 201–303（103 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486,UNP RESIDUES 43-122, 201-303, 325-486,UNP RESIDUES 43-122, 201-303, 325-486
Chain E 325–486（162 aa） Fragment：UNP RESIDUES 43-122, 201-303, 325-486,UNP RESIDUES 43-122, 201-303, 325-486,UNP RESIDUES 43-122, 201-303, 325-486
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；8% w/v PEG 8000, 0.2 M sodium acetate and 0.1 m sodium cacodylate, pH 6.5
Resolution 3.39 Å R-free 0.326

18 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q0ED31_9HIV1
Isoform —
PDB entities 2
Chains and sequence ranges Author chain G； PDBConstruct 1–80； UniProt 43–122

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 4p9h

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4p9h
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4p9h
Deposition date deposition_date2014-04-04
Structure title titleCrystal structure of 8ANC195 Fab in complex with gp120 of 93TH057 HIV-1 and soluble CD4 D1D2
Keywords keywordsIG FOLD, ANTI HIV, ANTIBODY, IMMUNE SYSTEM COMPLEX, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier36.18 Å
Radius of gyration Rg (electron density) rg_electron35.93 Å
Forward intensity I(0) i0179251000.00
Molecular weight molecular_weight104990.0 kDa
Excluded volume excluded_volume130220 ų
Envelope volume envelope_volume176910 ų
Hydration-shell volume shell_volume42128 ų
Envelope diameter envelope_diameter127.5 Å
Shell Rg shell_rg40.73 Å
Envelope Rg envelope_rg35.85 Å
Shape Rg shape_rg35.91 Å
Total Rg total_rg36.33 Å
Total atoms total_atoms7371
Residues n_residues911
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax118.5 Å
Rg (real space) rg_real36.28 Å
Rg uncertainty (real space) rg_real_error1.04 Å
I(0) (real space) i0_real1.7930e+08
I(0) uncertainty (real space) i0_real_error3.1050e+06
Rg (reciprocal space) rg_reciprocal36.22 Å
I(0) (reciprocal space) i0_reciprocal179200000.0000
Solution quality estimate total_estimate0.8808
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.7 Å
Skewness Skewness skewness0.365
Kurtosis Kurtosis kurtosis-0.446
Angular range angular_range— – 0.2200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18070000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.748
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (12)

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7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd4p9hc1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd4p9hc2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.3 — C2 set domains
Domain ID domain_idd4p9hl1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd4p9hl2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (7 domains)

Domain ID domain_id4p9hC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4p9hC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4p9hG01
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology40 — HIV Envelope Protein Gp120; Chain G
Homologous superfamily homologous superfamily20 — Human immunodeficiency virus 1, Gp160, envelope glycoprotein
Domain ID domain_id4p9hH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4p9hH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4p9hL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4p9hL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)