Current Protein Identity：P04578
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Difference tags compare only the current result set; every original PDB and assembly record remains separate.
Related-Structure Differences
Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.
| PDB Entry | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Experimental Method | Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1AIK HIV GP41 CORE STRUCTURE Deposited 1997-04-20 | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain C
623–656（34 aa）
Fragment：PROTEASE-RESISTANT CORE
Chain N
544–579（36 aa）
Fragment：PROTEASE-RESISTANT CORE
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；A 10 MG/ML STOCK WAS DILUTED 1:1 IN A SITTING DROP WITH 80 MM NH4CL, 20% PEG200, AND 50% ISOPROPANOL, AND THEN ALLOWED TO EQUILIBRATE AGAINST 80 MM NH4CL, 20% PEG200, AND 30% ISOPROPANOL., pH 6.0, vapor diffusion - sitting drop
|
Resolution 2.00 Å R-free 0.266 |
| 1DF4 INTERACTIONS BETWEEN HIV-1 GP41 CORE AND DETERGENTS AND THEIR IMPLICATIONS FOR MEMBRANE FUSION Deposited 1999-11-17 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
546–579（34 aa）
Fragment：RESIDUES 1 - 34 AND 41 - 68 CONNECTED BY A SIX-RESIDUE LINKER (SER-GLY-GLY-ARG- GLY-GLY)
Chain A
628–655（28 aa）
Fragment：RESIDUES 1 - 34 AND 41 - 68 CONNECTED BY A SIX-RESIDUE LINKER (SER-GLY-GLY-ARG- GLY-GLY)
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；SODIUM CITRATE, AMMONIUM DIHYDROGEN PHOSPHATE, BETA-OG, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.45 Å R-free 0.245 |
| 1DF5 INTERACTIONS BETWEEN HIV-1 GP41 CORE AND DETERGENTS AND THEIR IMPLICATIONS FOR MEMBRANE FUSION Deposited 1999-11-17 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
546–579（34 aa）
Fragment：RESIDUES 1 - 34 AND 41 - 68 CONNECTED BY A SIX-RESIDUE LINKER (SER-GLY-GLY-ARG-GLY-GLY)
Chain A
628–655（28 aa）
Fragment：RESIDUES 1 - 34 AND 41 - 68 CONNECTED BY A SIX-RESIDUE LINKER (SER-GLY-GLY-ARG-GLY-GLY)
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Potassium sodium tartrate, SDS, sodium hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.70 Å R-free 0.315 |
| 1DLB HELICAL INTERACTIONS IN THE HIV-1 GP41 CORE REVEALS STRUCTURAL BASIS FOR THE INHIBITORY ACTIVITY OF GP41 PEPTIDES Deposited 1999-12-09 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
546–579（34 aa）
Fragment：RESIDUES 1 - 34 AND 41 - 68 CONNECTED BY A SIX-RESIDUE LINKER (SER-GLY-GLY-ARG- GLY-GLY)
Chain A
628–655（28 aa）
Fragment：RESIDUES 1 - 34 AND 41 - 68 CONNECTED BY A SIX-RESIDUE LINKER (SER-GLY-GLY-ARG- GLY-GLY)
|
Mutation：Q65L Mutation：Q65L | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；PEG 4000, AMMONIUM SULPHATE, SODIUM ACETATE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.00 Å R-free 0.243 |
| 1G9M HIV-1 HXBC2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B Deposited 2000-11-24 | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain G
83–127（45 aa）
Fragment：CORE
Chain G
195–297（103 aa）
Fragment：CORE
Chain G
330–492（163 aa）
Fragment：CORE
|
Mutation：VARIABLE LOOPS SUBSTITUTED Mutation：VARIABLE LOOPS SUBSTITUTED Mutation：VARIABLE LOOPS SUBSTITUTED | 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 |
| 1GC1 HIV-1 GP120 CORE COMPLEXED WITH CD4 AND A NEUTRALIZING HUMAN ANTIBODY Deposited 1998-06-15 | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain G
83–127（45 aa）
Fragment：CORE
Chain G
195–297（103 aa）
Fragment：CORE
Chain G
330–492（163 aa）
Fragment：CORE
|
Mutation：(GARS) SUBSTITUTION AT THE N TERMINUS, GLY ALA GLY SUBSTITUTIONS FOR THE V1/V2 AND V3 LOOPS Mutation：(GARS) SUBSTITUTION AT THE N TERMINUS, GLY ALA GLY SUBSTITUTIONS FOR THE V1/V2 AND V3 LOOPS Mutation：(GARS) SUBSTITUTION AT THE N TERMINUS, GLY ALA GLY SUBSTITUTIONS FOR THE V1/V2 AND V3 LOOPS | 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 |
| 1GZL Crystal structure of C14linkmid/IQN17: a cross-linked inhibitor of HIV-1 entry bound to the gp41 hydrophobic pocket Deposited 2002-05-23 | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain A
565–581（17 aa）
Fragment：GP41 HYDROPHOBIC POCKET, RESIDUES 565-581, GCN4, RESIDUES 249-276
Chain C
628–639（12 aa）
Fragment：RESIDUES 628-639
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES | CL CHLORIDE ION × 3 N2P PENTANE-1,5-DIAMINE × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 8.6；16% ISOPROPANOL, 0.1 M TRIS, PH 8.6, 1 M (NH4)2SO4
|
Resolution 1.80 Å R-free 0.243 |
| 1GZL Crystal structure of C14linkmid/IQN17: a cross-linked inhibitor of HIV-1 entry bound to the gp41 hydrophobic pocket Deposited 2002-05-23 | Assembly 2 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain B
565–581（17 aa）
Fragment：GP41 HYDROPHOBIC POCKET, RESIDUES 565-581, GCN4, RESIDUES 249-276
Chain D
628–639（12 aa）
Fragment：RESIDUES 628-639
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES | CL CHLORIDE ION × 3 N2P PENTANE-1,5-DIAMINE × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 8.6；16% ISOPROPANOL, 0.1 M TRIS, PH 8.6, 1 M (NH4)2SO4
|
Resolution 1.80 Å R-free 0.243 |
| 1K33 Crystal structure analysis of the gp41 core mutant Deposited 2001-10-01 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
546–579（34 aa）
Fragment：gp41 ectodomain core
Chain A
628–655（28 aa）
Fragment：gp41 ectodomain core
|
Mutation：I48A Mutation：I48A | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.75 Å R-free 0.226 |
| 1K34 Crystal structure analysis of gp41 core mutant Deposited 2001-10-01 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
546–579（34 aa）
Fragment：gp41 ectodomain core
Chain A
628–655（28 aa）
Fragment：gp41 ectodomain core
|
Mutation：I55A Mutation：I55A | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.88 Å R-free 0.216 |
| 1MZI Solution ensemble structures of HIV-1 gp41 2F5 mAb epitope Deposited 2002-10-08 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
659–671（13 aa）
Fragment：13 residues 2F5 epitope
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 6.5；278 K；Ionic strength (raw mmCIF value) 50mM phosphate buffer；Pressure ambient
NMR sample composition
1.5mM peptide, 50mM phosphate buffer, pH 6.5 | 95% H2O/5% D2O
NMR sample composition
1.5mM peptide, 50mM phosphate buffer, pH 6.5 | 100% D2O
|
Resolution not provided |
| 1RZJ HIV-1 HXBC2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B Deposited 2003-12-24 | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain G
195–492（298 aa）
Fragment：CORE
|
Mutation：VARIABLE LOOPS SUBSTITUTED | 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 |
| 2CMR Crystal structure of the HIV-1 neutralizing antibody D5 Fab bound to the gp41 inner-core mimetic 5-helix Deposited 2006-05-11 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
543–582（40 aa）
Fragment：5-HELIX, RESIDUES 543-582 AND 625-662
Chain A
625–662（38 aa）
Fragment：5-HELIX, RESIDUES 543-582 AND 625-662
|
Not recorded | GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 8.5；18% (W/V) PEG 4000, 0.2 M TRI-SODIUM CITRATE DIHYDRATE, 0.1 M TRIS-HCL / PH = 8.5
|
Resolution 2.00 Å R-free 0.258 |
| 2ME1 HIV-1 gp41 clade B double alanine mutant Membrane Proximal External Region peptide in DPC micelle Deposited 2013-09-20 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
657–683（27 aa）
Fragment：membrane proximal external region (UNP residues 657-683)
|
Mutation：N671A/N674A | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 6.6；308 K；Ionic strength (raw mmCIF value) 0；Pressure ambient
NMR sample composition
1 mM [U-100% 13C; U-100% 15N] MPER-HXB2-AA, 100 mM [U-100% 2H] DPC, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1 mM [U-100% 15N] MPER-HXB2-AA, 100 mM [U-100% 2H] DPC, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1 mM MPER-HXB2-AA, 100 mM [U-100% 2H] DPC, 100% D2O | 100% D2O
NMR sample composition
1 mM [U-100% 13C; U-100% 15N] MPER-HXB2-AA, 100 mM [U-100% 2H] DPC, 20 mg/mL DNA nanotube, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2MG1 NMR assignment and structure of a peptide derived from the trans-membrane region of HIV-1 gp41 in the presence of hexafluoroisopropanol Deposited 2013-10-24 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
683–704（22 aa）
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 2；Pressure ambient
NMR sample composition
0.5 mM TMDp, 67.5 % H2O, 7.5 % [U-100% 2H] D2O, 25 % hexafluoroisopropanol, 2 mM HEPES, 0.1 mM DSS, hexafluoroisopropanol/water | hexafluoroisopropanol/water
|
Resolution not provided |
| 2NY7 HIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neutralizing CD4-Binding-Site Antibody b12 Deposited 2006-11-20 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain G
176–492（317 aa）
Fragment：CORE
|
Mutation：M95W, W96C, I109C, T257S, V275C, S334A, S375W, Q428C, A433M | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 | X-RAY DIFFRACTION | mmCIF provides none of the parsed conditions | Resolution 2.30 Å R-free 0.255 |
| 2NY7 HIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neutralizing CD4-Binding-Site Antibody b12 Deposited 2006-11-20 | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain G
176–492（317 aa）
Fragment：CORE
|
Mutation：M95W, W96C, I109C, T257S, V275C, S334A, S375W, Q428C, A433M | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 | X-RAY DIFFRACTION | mmCIF provides none of the parsed conditions | Resolution 2.30 Å R-free 0.255 |
| 2NY7 HIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neutralizing CD4-Binding-Site Antibody b12 Deposited 2006-11-20 | Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain G
176–492（317 aa）
Fragment：CORE
|
Mutation：M95W, W96C, I109C, T257S, V275C, S334A, S375W, Q428C, A433M | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 | X-RAY DIFFRACTION | mmCIF provides none of the parsed conditions | Resolution 2.30 Å R-free 0.255 |
| 2NY7 HIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neutralizing CD4-Binding-Site Antibody b12 Deposited 2006-11-20 | Assembly 4 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain G
176–492（317 aa）
Fragment：CORE
|
Mutation：M95W, W96C, I109C, T257S, V275C, S334A, S375W, Q428C, A433M | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 | X-RAY DIFFRACTION | mmCIF provides none of the parsed conditions | Resolution 2.30 Å R-free 0.255 |
| 2NY7 HIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neutralizing CD4-Binding-Site Antibody b12 Deposited 2006-11-20 | Assembly 5 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain G
176–492（317 aa）
Fragment：CORE
|
Mutation：M95W, W96C, I109C, T257S, V275C, S334A, S375W, Q428C, A433M | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 | X-RAY DIFFRACTION | mmCIF provides none of the parsed conditions | Resolution 2.30 Å R-free 0.255 |
| 2PV6 HIV-1 gp41 Membrane Proximal Ectodomain Region peptide in DPC micelle Deposited 2007-05-09 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
662–683（22 aa）
Fragment：residues 662-683
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 6.6；308 K；Ionic strength (raw mmCIF value) no salt；Pressure ambient
NMR sample composition
1mM U-15N,13C MPER + 100mM d38 DPC, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1mM U-15N MPER + 100mM d38 DPC, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1mM unlabeled MPER + 100mM d38 DPC, 100% D2O | 100% D2O
|
Resolution not provided |
| 2X7R Crystal structure of a late fusion intermediate of HIV-1 gp41 Deposited 2010-03-03 | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
629–683（55 aa）
Fragment：EXTRA CELLULAR DOMAIN, RESIDUES 629-683
Chain N
528–581（54 aa）
Fragment：EXTRA CELLULAR DOMAIN, RESIDUES 534-581
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 6；0.1M CITRIC ACID PH 6, 60% MPD
|
Resolution 2.00 Å R-free 0.214 |
| 2X7R Crystal structure of a late fusion intermediate of HIV-1 gp41 Deposited 2010-03-03 | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
528–581（54 aa）
Fragment：EXTRA CELLULAR DOMAIN, RESIDUES 534-581
Chain E
629–683（55 aa）
Fragment：EXTRA CELLULAR DOMAIN, RESIDUES 629-683
|
Not recorded | NA SODIUM ION × 1 CL CHLORIDE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 6；0.1M CITRIC ACID PH 6, 60% MPD
|
Resolution 2.00 Å R-free 0.214 |
| 2X7R Crystal structure of a late fusion intermediate of HIV-1 gp41 Deposited 2010-03-03 | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
528–581（54 aa）
Fragment：EXTRA CELLULAR DOMAIN, RESIDUES 534-581
Chain B
629–683（55 aa）
Fragment：EXTRA CELLULAR DOMAIN, RESIDUES 629-683
|
Not recorded | NA SODIUM ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 6；0.1M CITRIC ACID PH 6, 60% MPD
|
Resolution 2.00 Å R-free 0.214 |
| 2XRA crystal structure of the HK20 Fab in complex with a gp41 mimetic 5- Helix Deposited 2010-09-13 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
543–582（40 aa）
Fragment：5-HELIX INNER-CORE MIMETIC COMPRISED OF REPEATS OF RESIDUES 543-582 AND 625-662
Chain A
625–662（38 aa）
Fragment：5-HELIX INNER-CORE MIMETIC COMPRISED OF REPEATS OF RESIDUES 543-582 AND 625-662
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.5；0.1 M HEPES PH 7.5, 0.2 M AMMONIUM SULPHATE, 25% PEG 3350 (W/V)
|
Resolution 2.30 Å R-free 0.279 |
| 2ZZO Crystal structure of the complex between GP41 fragment N36 and fusion inhibitor C34/S138A Deposited 2009-02-20 | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain C
628–661（34 aa）
Fragment：FUSION INHIBITOR PEPTIDE C34, UNP residues 628-661
Chain N
546–581（36 aa）
Fragment：GP41 FRAGMENT N36, UNP residues 546-581
|
Mutation：S138A Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 4；293 K；100MM SODIUM ACETATE BUFFER, PH4.0, 400MM MAGNESIUM CHLORIDE, 12% ETHANOL, pH 4.00, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.20 Å R-free 0.283 |
| 3DNL Molecular structure for the HIV-1 gp120 trimer in the b12-bound state Deposited 2008-07-02 | Assembly 1 Protein homooligomer Homooligomer；Protein × 9 PDB declaration: nonameric（9） Consistent with protein count |
Chain A
90–124（35 aa）
Fragment：Core: Residues 90-124
Chain B
198–297（100 aa）
Fragment：Core: Residues 198-396
Chain B
330–396（67 aa）
Fragment：Core: Residues 198-396
Chain C
410–492（83 aa）
Fragment：Core: Residues 410-492
Chain D
90–124（35 aa）
Fragment：Core: Residues 90-124
Chain E
198–297（100 aa）
Fragment：Core: Residues 198-396
Chain E
330–396（67 aa）
Fragment：Core: Residues 198-396
Chain F
410–492（83 aa）
Fragment：Core: Residues 410-492
Chain G
90–124（35 aa）
Fragment：Core: Residues 90-124
Chain H
198–297（100 aa）
Fragment：Core: Residues 198-396
Chain H
330–396（67 aa）
Fragment：Core: Residues 198-396
Chain I
410–492（83 aa）
Fragment：Core: Residues 410-492
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
0.01 M Tris-HCl, 0.1 M NaCl, 1 mM EDTA；pH 7.2；0.01 M Tris-HCl, 0.1 M NaCl, 1 mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE；Ethane 77K 100%RH Vitrobot
|
Resolution 20.00 Å |
| 3DNN Molecular structure for the HIV-1 gp120 trimer in the unliganded state Deposited 2008-07-02 | Assembly 1 Protein homooligomer Homooligomer；Protein × 9 PDB declaration: nonameric（9） Consistent with protein count |
Chain A
90–124（35 aa）
Fragment：Core: Residues 90-124
Chain B
198–297（100 aa）
Fragment：Core: Residues 198-396
Chain B
330–396（67 aa）
Fragment：Core: Residues 198-396
Chain C
410–492（83 aa）
Fragment：Core: Residues 410-492
Chain D
90–124（35 aa）
Fragment：Core: Residues 90-124
Chain E
198–297（100 aa）
Fragment：Core: Residues 198-396
Chain E
330–396（67 aa）
Fragment：Core: Residues 198-396
Chain F
410–492（83 aa）
Fragment：Core: Residues 410-492
Chain G
90–124（35 aa）
Fragment：Core: Residues 90-124
Chain H
198–297（100 aa）
Fragment：Core: Residues 198-396
Chain H
330–396（67 aa）
Fragment：Core: Residues 198-396
Chain I
410–492（83 aa）
Fragment：Core: Residues 410-492
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
0.01 M Tris-HCl, 0.1 M NaCl, 1 mM EDTA；pH 7.2；0.01 M Tris-HCl, 0.1 M NaCl, 1 mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE；Ethane 77K 100%RH Vitrobot
|
Resolution 20.00 Å |
| 3DNO Molecular structure for the HIV-1 gp120 trimer in the CD4-bound state Deposited 2008-07-02 | Assembly 1 Protein homooligomer Homooligomer；Protein × 9 PDB declaration: nonameric（9） Consistent with protein count |
Chain A
90–124（35 aa）
Fragment：Core: Residues 90-124
Chain B
198–297（100 aa）
Fragment：Core: Residues 198-396
Chain B
330–396（67 aa）
Fragment：Core: Residues 198-396
Chain C
410–492（83 aa）
Fragment：Core: Residues 410-492
Chain D
90–124（35 aa）
Fragment：Core: Residues 90-124
Chain E
198–297（100 aa）
Fragment：Core: Residues 198-396
Chain E
330–396（67 aa）
Fragment：Core: Residues 198-396
Chain F
410–492（83 aa）
Fragment：Core: Residues 410-492
Chain G
90–124（35 aa）
Fragment：Core: Residues 90-124
Chain H
198–297（100 aa）
Fragment：Core: Residues 198-396
Chain H
330–396（67 aa）
Fragment：Core: Residues 198-396
Chain I
410–492（83 aa）
Fragment：Core: Residues 410-492
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
0.01 M Tris-HCl, 0.1 M NaCl, 1 mM EDTA；pH 7.2；0.01 M Tris-HCl, 0.1 M NaCl, 1 mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE；Ethane 77K 100%RH Vitrobot
|
Resolution 20.00 Å |
| 3J70 Model of gp120, including variable regions, in complex with CD4 and 17b Deposited 2014-04-22 | Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein count |
Chain D
31–500（470 aa）
Fragment：UNP residues 31-500
Chain P
31–500（470 aa）
Fragment：UNP residues 31-500
Chain U
31–500（470 aa）
Fragment：UNP residues 31-500
|
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 |
| 3TYG Crystal structure of broad and potent HIV-1 neutralizing antibody PGT128 in complex with a glycosylated engineered gp120 outer domain with miniV3 (eODmV3) Deposited 2011-09-25 | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
412–419（8 aa）
Chain A
445–477（33 aa）
Chain A
254–297（44 aa）
Chain A
330–401（72 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；24% PEG 3350, 0.29M CaCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 3.25 Å R-free 0.257 |
| 5C0R Crystal Structure of a Generation 3 Influenza Hemagglutinin Stabilized Stem Complexed with the Broadly Neutralizing Antibody C179 Deposited 2015-06-12 | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric（9） Consistent with protein count |
Chain A
628–654（27 aa）
Fragment：UNP Q6WG00 residues 18-49, 328-402, 436-517, UNP P04578 residues 546-577, 628-654 and UNP D9IEJ2 residues 458-485
Chain A
546–577（32 aa）
Fragment：UNP Q6WG00 residues 18-49, 328-402, 436-517, UNP P04578 residues 546-577, 628-654 and UNP D9IEJ2 residues 458-485
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；15% (w/v) PEG 1500, 5% (v/v) MPD, 200 mM ammonium chloride, 100 mM Tris, pH 8.5
|
Resolution 3.19 Å R-free 0.251 |
| 5C0S Crystal structure of a generation 4 influenza hemagglutinin stabilized stem in complex with the broadly neutralizing antibody CR6261 Deposited 2015-06-12 | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric（9） Consistent with protein count |
Chain A
628–654（27 aa）
Fragment：UNP Q6WG00 residues 18-49, 328-402, 436-517, UNP P04578 residues 546-577, 628-654 and UNP D9IEJ2 residues 458-485
Chain A
546–577（32 aa）
Fragment：UNP Q6WG00 residues 18-49, 328-402, 436-517, UNP P04578 residues 546-577, 628-654 and UNP D9IEJ2 residues 458-485
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；7% (w/v) PEG 4000, 4.5% (v/v) isopropanol, 100 mM imidazole, pH 6.5
|
Resolution 4.30 Å R-free 0.310 |
| 5HM1 Llama VHH 2E7 in complex with gp41 Deposited 2016-01-15 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
582–596（15 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1 M Hepes pH 7.0
30% PEG 6000
|
Resolution 2.96 Å R-free 0.249 |
| 5HM1 Llama VHH 2E7 in complex with gp41 Deposited 2016-01-15 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain E
582–596（15 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1 M Hepes pH 7.0
30% PEG 6000
|
Resolution 2.96 Å R-free 0.249 |
| 5HM1 Llama VHH 2E7 in complex with gp41 Deposited 2016-01-15 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
582–596（15 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1 M Hepes pH 7.0
30% PEG 6000
|
Resolution 2.96 Å R-free 0.249 |
| 5KA5 HIV-1 gp41 variant V549E resistance mutation Deposited 2016-06-01 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
543–582（40 aa）
Fragment：UNP residues 543-582 and 625-661 linked via GGRGG
Chain A
625–661（37 aa）
Fragment：UNP residues 543-582 and 625-661 linked via GGRGG
|
Mutation：V549E Mutation：V549E | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；3M Sodium chloride, 0.1M Sodium Acetate
Sample concentration: 6 mg/ml
|
Resolution 1.80 Å R-free 0.223 |
| 5KA6 HIV-1 gp41 variant Q552R and L555M resistance mutations Deposited 2016-06-01 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
543–582（40 aa）
Fragment：UNP residues 543-582 and 625-661 linked via GGRGG
Chain A
625–661（37 aa）
Fragment：UNP residues 543-582 and 625-661 linked via GGRGG
Chain B
543–582（40 aa）
Fragment：UNP residues 543-582 and 625-661 linked via GGRGG
Chain B
625–661（37 aa）
Fragment：UNP residues 543-582 and 625-661 linked via GGRGG
Chain C
543–582（40 aa）
Fragment：UNP residues 543-582 and 625-661 linked via GGRGG
Chain C
625–661（37 aa）
Fragment：UNP residues 543-582 and 625-661 linked via GGRGG
|
Mutation：Q552R, L555M Mutation：Q552R, L555M Mutation：Q552R, L555M Mutation：Q552R, L555M Mutation：Q552R, L555M Mutation：Q552R, L555M | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 8000, 0.3M Calcium Acetate, 0.1M Sodium Cacodylate
Sample concentration: 6.35 mg/ml
|
Resolution 1.85 Å R-free 0.278 |
| 6DLN Oligomeric Structure of the HIV gp41 MPER-TMD in Phospholipid Bilayers Deposited 2018-06-01 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
665–703（39 aa）
Fragment：residues 665-703
Chain B
665–703（39 aa）
Fragment：residues 665-703
Chain C
665–703（39 aa）
Fragment：residues 665-703
|
Not recorded | No recorded non-water small molecule | SOLID-STATE NMR |
NMR measurement conditions
pH 7.5；263 K；Pressure 1
NMR measurement conditions
pH 7.5；233 K；Pressure 1
NMR sample composition
33 % w/w 4-19F-F699 HIV gp41 MPER-TMD, reconstituted into the virus mimetic membrane (POPC:POPE:POPS:sphingomyelin: cholesterol = 30:15:15:10:30), 10 mM HEPES buffer pH 7.5 | 10 mM HEPES buffer pH 7.5
NMR sample composition
33 % w/w [U-13C; U-15N]-L684,I686, G694, 19F-5F-W678, 19F-4F-F699 HIV gp41 MPER-TMD, reconstituted into the virus mimetic membrane (POPC:POPE:POPS:sphingomyelin: cholesterol = 30:15:15:10:30), 10 mM HEPES buffer pH 7.5 | 10 mM HEPES buffer pH 7.5
NMR sample composition
33 % w/w [U-13C; U-15N]-L669,I686, A700, 13C'-G694, 19F-5F-W680 HIV gp41 MPER-TMD, reconstituted into the virus mimetic membrane (POPC:POPE:POPS:sphingomyelin: cholesterol = 30:15:15:10:30), 10 mM HEPES buffer pH 7.5 | 10 mM HEPES buffer pH 7.5
|
Resolution not provided |
| 6PSA PIE12 D-PEPTIDE AGAINST HIV ENTRY (IN COMPLEX WITH IQN17 Q577R RESISTANCE MUTANT) Deposited 2019-07-12 | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain A
565–581（17 aa）
Fragment：GP41 HYDROPHOBIC POCKET, RESIDUES 565-581, GCN4, RESIDUES 249-276
|
Mutation：Q577R Non-standard monomer：Yes (specific site not provided by mmCIF) | CL CHLORIDE ION × 6 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；294 K；HAMPTON RESEARCH SALT RX SCREEN, CONDITION B4 - 1.8M AMMONIUM CITRATE DIBASIC, 0.1 M SODIUM ACETATE TRIHYDRATE, PH 4.6
|
Resolution 1.30 Å R-free 0.217 |
| 8TQ7 Crystal structure of Fab.34.2.12 in complex with MHC-I (H2-Dd) Deposited 2023-08-06 | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric（10） Consistent with protein count |
Chain E
311–320（10 aa）
Fragment：HV1: HIV-1 P18-I10 (UNP residues 311-320)
Chain P
311–320（10 aa）
Fragment：HV1: HIV-1 P18-I10 (UNP residues 311-320)
|
Not recorded | EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；12% PEG8000, 0.1 M MES, pH 6.5
|
Resolution 2.80 Å R-free 0.271 |
| 8TQ8 Crystal structure of Fab.34.5.8 in complex with MHC-I (H2-Dd) Deposited 2023-08-06 | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count |
Chain P
311–320（10 aa）
Fragment：HV1: HIV-1 P18-I10 (UNP residues 311-320)
|
Not recorded | GOL GLYCEROL × 3 EDO 1,2-ETHANEDIOL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；18% PEG4000, 0.1 M MES, pH 6.0, 0.12 M calcium acetate
|
Resolution 2.69 Å R-free 0.242 |
| 8TQ8 Crystal structure of Fab.34.5.8 in complex with MHC-I (H2-Dd) Deposited 2023-08-06 | Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count |
Chain E
311–320（10 aa）
Fragment：HV1: HIV-1 P18-I10 (UNP residues 311-320)
|
Not recorded | GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；18% PEG4000, 0.1 M MES, pH 6.0, 0.12 M calcium acetate
|
Resolution 2.69 Å R-free 0.242 |
| 8TQ9 Crystal structure of Fab.S19.8 in complex with MHC-I (H2-Dd) Deposited 2023-08-06 | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count |
Chain P
311–320（10 aa）
Fragment：HV1: HIV-1 P18-I10 (UNP residues 311-320)
|
Not recorded | SO4 SULFATE ION × 1 GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；0.5 M ammonium sulfate, 0.1 M sodium citrate, pH 5.6, 1.0 M lithium sulfate
|
Resolution 2.90 Å R-free 0.240 |
| 8W2Y Structure and interactions of HIV-1 gp41 CHR-NHR reverse hairpin constructs reveal molecular determinants of antiviral activity Deposited 2024-02-21 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
542–591（50 aa）
|
Not recorded | GOL GLYCEROL × 3 SO4 SULFATE ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.4；293 K；0.1M lithium sulfate, 0.1M sodium citrate trihydrate at pH 6.4 and 25% PEG-1500
|
Resolution 1.63 Å R-free 0.291 |
| 8W32 Structure and interactions of HIV-1 gp41 CHR-NHR reverse hairpin constructs reveal molecular determinants of antiviral activity Deposited 2024-02-21 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
542–591（50 aa）
|
Not recorded | SO4 SULFATE ION × 3 GOL GLYCEROL × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.4；293 K；0.1M lithium sulfate, 0.1M sodium citrate trihydrate at pH 6.4 and 25% PEG-1500
|
Resolution 1.72 Å R-free 0.290 |
| 8W37 Structure and interactions of HIV-1 gp41 CHR-NHR reverse hairpin constructs reveal molecular determinants of antiviral activity Deposited 2024-02-22 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
542–591（50 aa）
|
Not recorded | SO4 SULFATE ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.4；293 K；0.1M lithium sulfate, 0.1M sodium citrate trihydrate at pH 6.4 and 25% PEG-1500
|
Resolution 2.07 Å R-free 0.268 |
| 9ARN Structure and interactions of HIV-1 gp41 CHR-NHR reverse hairpin constructs reveal molecular determinants of antiviral activity Deposited 2024-02-23 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
542–591（50 aa）
Fragment：residues 542-591 (Uniprot numbering), plus N-terminal extension
|
Not recorded | SO4 SULFATE ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.4；293 K；0.1M lithium sulfate, 0.1M sodium citrate trihydrate at pH 6.4 and 25% PEG-1500
|
Resolution 1.41 Å R-free 0.291 |
| 9ARP Structure and interactions of HIV-1 gp41 CHR-NHR reverse hairpin constructs reveal molecular determinants of antiviral activity Deposited 2024-02-23 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
542–591（50 aa）
Fragment：residues 542-591 (Uniprot numbering), with N-terminal extension
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；200mM ammonium sulfate, 100mM sodium acetate,
25% w/v PEG 4000 at pH 4.6
|
Resolution 2.04 Å R-free 0.369 |
| 9ARP Structure and interactions of HIV-1 gp41 CHR-NHR reverse hairpin constructs reveal molecular determinants of antiviral activity Deposited 2024-02-23 | Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
542–591（50 aa）
Fragment：residues 542-591 (Uniprot numbering), with N-terminal extension
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；200mM ammonium sulfate, 100mM sodium acetate,
25% w/v PEG 4000 at pH 4.6
|
Resolution 2.04 Å R-free 0.369 |