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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：P03407 New Search
8PDB entries
14Biological assembly
18chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion 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
3RBB HIV-1 NEF protein in complex with engineered HCK SH3 domain Deposited 2011-03-29 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 45–210（166 aa）
Mutation：I47M, T48A, C59S, C210A EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes, 8% ethylene glycol, 22% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.35 Å R-free 0.245
3RBB HIV-1 NEF protein in complex with engineered HCK SH3 domain Deposited 2011-03-29 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain C 45–210（166 aa）
Mutation：I47M, T48A, C59S, C210A EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes, 8% ethylene glycol, 22% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.35 Å R-free 0.245
3REA HIV-1 Nef protein in complex with engineered Hck-SH3 domain Deposited 2011-04-04 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 45–210（166 aa）
Mutation：I47M, T48A, C59S, C210A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；285 K；100 mM Tris buffer, 5% ethylne glycol, 10% PEG 8000, 0.2 M MgCl2, 15 mM MnCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Resolution 2.00 Å R-free 0.205
3REA HIV-1 Nef protein in complex with engineered Hck-SH3 domain Deposited 2011-04-04 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain C 45–210（166 aa）
Mutation：I47M, T48A, C59S, C210A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；285 K；100 mM Tris buffer, 5% ethylne glycol, 10% PEG 8000, 0.2 M MgCl2, 15 mM MnCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Resolution 2.00 Å R-free 0.205
3REB HIV-1 Nef protein in complex with engineered Hck-SH3 domain Deposited 2011-04-04 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 45–210（166 aa）
Mutation：I47M, T48A, C59S, C210A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；285 K；100 mM Hepes, 0.05 M sodium citrate, 15% isopropanol, 30% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Resolution 3.45 Å R-free 0.243
3REB HIV-1 Nef protein in complex with engineered Hck-SH3 domain Deposited 2011-04-04 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain C 45–210（166 aa）
Mutation：I47M, T48A, C59S, C210A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；285 K；100 mM Hepes, 0.05 M sodium citrate, 15% isopropanol, 30% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Resolution 3.45 Å R-free 0.243
4ORZ HIV-1 Nef protein in complex with single domain antibody sdAb19 and an engineered Hck SH3 domain Deposited 2014-02-12 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain B 45–210（166 aa） Fragment：Nef protein, UNP residues 45-210
Mutation：I47M, T48A, C59S, C210A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；About 0.1 micro L of protein solution at 10 mg/ml concentration was mixed with 0.1 micro L of reservoir solution from a 70 L reservoir in 96-well Hampton 3553 crystallization plates. Initial crystals of NefSF2 sdAb19 SH3B6 could be obtained in 0.2 M potassium formate and 20% polyethylene glycol (PEG) 3350. Crystal conditions were optimized to 0.2 M potassium formate, 17.5% polyethylene glycol (PEG) 3350 and 0.35 M ammonium chloride grown by hanging-drop vapor diffusion in Linbro crystallization plates. , pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å R-free 0.236
4U5W Crystal Structure of HIV-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains Deposited 2014-07-25 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 62–209（148 aa） Fragment：UNP residues 62-209
Chain C 62–209（148 aa） Fragment：UNP residues 62-209
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 3 IOD IODIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277.15 K；0.09 M ADA, pH 6.5, 10.8% (v/v) 2-methyl-2,4-pentanediol, 100 mM NaI
Resolution 1.86 Å R-free 0.195
6B72 A novel HIV-1 Nef dimer interface induced by a single octyl-glucoside molecule Deposited 2017-10-03 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 57–207（151 aa） Fragment：UNP residues 57-207
Chain B 57–207（151 aa） Fragment：UNP residues 57-207
Not recorded BOG octyl beta-D-glucopyranoside × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；18%-20% PEG5000 MME, 0.1 M Bis-Tris propane, pH 8.0, 5% glycerol
Resolution 3.20 Å R-free 0.251
6B72 A novel HIV-1 Nef dimer interface induced by a single octyl-glucoside molecule Deposited 2017-10-03 Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain C 57–207（151 aa） Fragment：UNP residues 57-207
Chain E 57–207（151 aa） Fragment：UNP residues 57-207
Not recorded BOG octyl beta-D-glucopyranoside × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；18%-20% PEG5000 MME, 0.1 M Bis-Tris propane, pH 8.0, 5% glycerol
Resolution 3.20 Å R-free 0.251
6B72 A novel HIV-1 Nef dimer interface induced by a single octyl-glucoside molecule Deposited 2017-10-03 Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain D 57–207（151 aa） Fragment：UNP residues 57-207
Chain F 57–207（151 aa） Fragment：UNP residues 57-207
Not recorded BOG octyl beta-D-glucopyranoside × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；18%-20% PEG5000 MME, 0.1 M Bis-Tris propane, pH 8.0, 5% glycerol
Resolution 3.20 Å R-free 0.251
7D7S HIV-1 SF2 Nef in complex with the Fyn SH3 R96I mutant Deposited 2020-10-05 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 1–209（209 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；0.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；0.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；0.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000
Resolution 3.32 Å R-free 0.300
7D7S HIV-1 SF2 Nef in complex with the Fyn SH3 R96I mutant Deposited 2020-10-05 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 1–209（209 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；0.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；0.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；0.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000
Resolution 3.32 Å R-free 0.300
8F2P Nef SF2 dimerization mutant bound to Hck SH3 Deposited 2022-11-08 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 62–209（148 aa） Fragment：Nef SF2 core domain (UNP residues 62-209)
Mutation：L116D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.1 M sodium chloride, 0.1 M sodium acetate, pH 4.6, 12% v/v MPD
Resolution 2.63 Å R-free 0.252

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.