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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：B3UEZ6 New Search
15PDB entries
15Biological assembly
39chain/assembly records
Main Difference Dimensions in This Set
Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

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
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 Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein count
Chain A 516–668（153 aa）
Chain B 516–668（153 aa）
Chain D 516–668（153 aa）
Mutation：I559P, T605C Mutation：I559P, T605C Mutation：I559P, T605C 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
5VN8 Cryo-EM model of B41 SOSIP.664 in complex with fragment antigen binding variable domain of b12 Deposited 2017-04-28 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric（12） Consistent with protein count
Chain A 516–668（153 aa）
Chain B 516–668（153 aa）
Chain C 516–668（153 aa）
Mutation：I559P, T605C Mutation：I559P, T605C Mutation：I559P, T605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 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 3.60 Å
6CH9 Crystal structure of a natively-glycosylated B41 SOSIP.664 HIV-1 Envelope Trimer in complex with the broadly-neutralizing antibodies BG18 and 35O22 Deposited 2018-02-22 Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric（18） Consistent with protein count
Chain B 516–668（153 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；5% Tacismate pH 8.0, 15% PEG 3350
Resolution 4.85 Å R-free 0.292
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 Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 21-meric（21） Consistent with protein count
Chain A 516–668（153 aa）
Chain B 516–668（153 aa）
Chain C 516–668（153 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
6MUF Crystal Structure of HIV-1 B41 SOSIP.664 Prefusion Env Trimer in Complex with Human Antibodies 3H109L and 35O22 at 3.4 Angstrom Deposited 2018-10-23 Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric（18） Consistent with protein count
Chain B 516–668（153 aa） Fragment：gp41
Mutation：I559P, A605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；298 K；90mM Na Acetate pH5.5 6% PEG8,000 3% PEG400 450mM NaCl
Resolution 2.91 Å R-free 0.297
6MUG Crystal Structure of HIV-1 B41 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor BMS-386150 in Complex with Human Antibodies 3H109L and 35O22 at 3.8 Angstrom Deposited 2018-10-23 Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric（18） Consistent with protein count
Chain B 516–668（153 aa） Fragment：gp41
Mutation：I559P, A605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 42 JYS 1-[4-(benzenecarbonyl)piperazin-1-yl]-2-(4-bromo-7-fluoro-1H-indol-3-yl)ethane-1,2-dione × 3 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；298 K；60mM Na Acetate pH5.5 4% PEG8,000 2%PEG400 300mM NaCl
Resolution 2.95 Å R-free 0.289
6OKP B41 SOSIP.664 in complex with the silent-face antibody SF12 and V3-targeting antibody 10-1074 Deposited 2019-04-14 Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: tetradecameric（14） Consistent with protein count
Chain A 516–668（153 aa） Fragment：UNP residues 516-668
Chain B 516–668（153 aa） Fragment：UNP residues 516-668
Chain C 516–668（153 aa） Fragment：UNP residues 516-668
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；0 blot force, 3 second blot time, 3 uL sample added to freshly glow-discharged grids
Resolution 3.28 Å
6OPN CD4- and 17-bound HIV-1 Env B41 SOSIP in complex with small molecule GO35 Deposited 2019-04-25 Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric（9） Consistent with protein count
Chain B 516–668（153 aa）
Chain E 516–668（153 aa）
Chain H 516–668（153 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 Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein count
Chain B 516–668（153 aa）
Chain F 516–668（153 aa）
Chain M 516–668（153 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 Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein count
Chain B 516–668（153 aa）
Chain E 516–668（153 aa）
Chain K 516–668（153 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 Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein count
Chain B 516–668（153 aa）
Chain F 516–668（153 aa）
Chain G 516–668（153 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
6U59 HIV-1 B41 SOSIP.664 in complex with rabbit antibody 13B Deposited 2019-08-27 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric（12） Consistent with protein count
Chain B 516–668（153 aa）
Chain D 516–668（153 aa）
Chain I 516–668（153 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Detergent was added to sample shortly prior to freezing.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.86 Å
6X5B Symmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with small molecule GO52 Deposited 2020-05-25 Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein count
Chain B 516–668（153 aa）
Chain E 516–668（153 aa）
Chain K 516–668（153 aa）
Mutation：I559P, T605C Mutation：I559P, T605C Mutation：I559P, T605C 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 Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric（9） Consistent with protein count
Chain B 516–668（153 aa）
Chain F 516–668（153 aa）
Chain G 516–668（153 aa）
Mutation：I559P, T605C Mutation：I559P, T605C Mutation：I559P, T605C 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
8D5C anti-HIV-1 gp120-sCD4 complex antibody CG10 Fab in complex with B41-sCD4 Deposited 2022-06-04 Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein count
Chain X 516–668（153 aa）
Chain Y 516–668（153 aa）
Chain Z 516–668（153 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

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.