1cdi

STRUCTURES OF AN HIV AND MHC BINDING FRAGMENT FROM HUMAN CD4 AS REFINED IN TWO CRYSTAL LATTICES

Method: X-RAY DIFFRACTION D_max: 72.5 Å Quality: REASONABLE

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1. Protein Identity and Related Structures Protein Identity & Related Structures

T CELL SURFACE GLYCOPROTEIN CD4

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 23–203	Not recorded	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.90 Å

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 1CDI	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 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
1CDJ STRUCTURE OF T-CELL SURFACE GLYCOPROTEIN CD4 Deposited 1996-11-11	Different construct Different oligomeric state 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 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 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 oligomeric state 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 oligomeric state 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 oligomeric state 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 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 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 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 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 oligomeric state 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 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 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 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 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 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
4P9H Crystal structure of 8ANC195 Fab in complex with gp120 of 93TH057 HIV-1 and soluble CD4 D1D2 Deposited 2014-04-04	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 26–207（182 aa） Fragment：CD4 D1D2	Mutation：K75T	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
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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 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 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 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 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 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 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 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 oligomeric state 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 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 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 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 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 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 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 A； PDBConstruct 1–179； UniProt 23–203

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1cdi
Deposition date deposition_date	1994-01-26
Structure title title	STRUCTURES OF AN HIV AND MHC BINDING FRAGMENT FROM HUMAN CD4 AS REFINED IN TWO CRYSTAL LATTICES
Keywords keywords	T-CELL SURFACE GLYCOPROTEIN; T-CELL SURFACE GLYCOPROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.92 Å
Radius of gyration Rg (electron density) rg_electron	20.30 Å
Forward intensity I(0) i0	7280070.00
Molecular weight molecular_weight	19789.0 kDa
Excluded volume excluded_volume	24815 Å³
Envelope volume envelope_volume	29549 Å³
Hydration-shell volume shell_volume	13665 Å³
Envelope diameter envelope_diameter	73.4 Å
Shell Rg shell_rg	24.60 Å
Envelope Rg envelope_rg	20.42 Å
Shape Rg shape_rg	20.31 Å
Total Rg total_rg	20.96 Å
Total atoms total_atoms	1390
Residues n_residues	179
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	72.5 Å
Rg (real space) rg_real	21.14 Å
Rg uncertainty (real space) rg_real_error	0.58 Å
I(0) (real space) i0_real	7.2800e+06
I(0) uncertainty (real space) i0_real_error	9.3470e+04
Rg (reciprocal space) rg_reciprocal	21.10 Å
I(0) (reciprocal space) i0_reciprocal	7280000.0000
Solution quality estimate total_estimate	0.6095
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.9 Å
Skewness Skewness skewness	0.528
Kurtosis Kurtosis kurtosis	-0.431
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2561000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.614; Stabil: 1.000; Sysdev: 0.177; Positv: 1.000; Valcen: 0.569; Smooth: 0.979

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1cdia1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1cdia2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.3 — C2 set domains

CATH v4.4 (2 domains)

Domain ID domain_id	1cdiA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1cdiA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	133.550 Å
Unit-cell length b length_b	32.270 Å
Unit-cell length c length_c	46.070 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.12 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1830
R_work r_work	0.1830
R_free r_free	—

Description description	T CELL SURFACE GLYCOPROTEIN CD4
Molecular weight formula_weight	19826.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1390

STRUCTURES OF AN HIV AND MHC BINDING FRAGMENT FROM HUMAN CD4 AS REFINED IN TWO CRYSTAL LATTICES

1. Protein Identity and Related Structures Protein Identity & Related Structures

T CELL SURFACE GLYCOPROTEIN CD4

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

fit	/app/data/saxs_computation/cd/1cdi/1cdi.fit
pddf	/app/data/pr_computation/cd/1cdi/1cdi.pr.out
profile	/app/data/saxs_computation/cd/1cdi/1cdi.dat