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6iwb

Crystal structure of a computationally designed protein (LD3) in complex with BCL-2

Method: X-RAY DIFFRACTION Dmax: 86.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Apolipoprotein E

Homo sapiens

UniProt P02649

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 41–186 Not recorded Apoptosis regulator Bcl-2,Apoptosis regulator Bcl-2 × 1 （P10415） SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295.15 K；17% PEG2000, 0.1M Sodium Succinate (pH 5.5), 0.32M Ammonium Sulfate Resolution 2.50 Å R-free 0.275
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 41–186 Not recorded Apoptosis regulator Bcl-2,Apoptosis regulator Bcl-2 × 1 （P10415） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295.15 K；17% PEG2000, 0.1M Sodium Succinate (pH 5.5), 0.32M Ammonium Sulfate Resolution 2.50 Å R-free 0.275

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 6IWB Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B68 APOLIPOPROTEIN E4 (APOE4), 22K FRAGMENT Deposited 1999-01-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 19–209（191 aa） Fragment：22K FRAGMENT, ISOFORM E4, RECEPTOR BINDING DOMAIN, RESIDUES 1-191
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；WELL : 28% PEG 400, 20MM NAOAC, PH 6.0, 0.1% BME PROTEIN SOLN: 40MM (NH4)H(CO3), 7MG/ML PROTEIN DROPS : WELL/PROTEIN 1/3, ROOM TEMPERATURE, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.255
1BZ4 APOLIPOPROTEIN E3 (APO-E3), TRUNCATION MUTANT 165 Deposited 1998-11-05 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 40–183（144 aa） Fragment：22K FRAGMENT, RECEPTOR BINDING DOMAIN, RESIDUES 1-165, TRUNCATION AT RESIDUE 165
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；RT, 50MM NA-CACODYLATE, PH 5.6, 20-25% PEG 400, 1% 2-ME. NOTE : W/O 2-ME, ANOTHER ORTHORHOMBIC FORM APPEARS (SEE PDB ENTRY 1oR2).
Resolution 1.85 Å R-free 0.245
1EA8 Apolipoprotein E3 22kD fragment LYS146GLU mutant Deposited 2001-07-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 19–209（191 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 1-191
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；50MM NA-CACODYLATE, PH 5.6, ORTHORHOMBIC FORM ORTHO-2 APPEARS (SEE PDB ENTRY 1OR2).
Resolution 1.95 Å R-free 0.258
1GS9 Apolipoprotein E4, 22k domain Deposited 2002-01-02 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 19–183（165 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 1-165
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；50MM NA-CACODYLATE, PH 5.6, 20-25% PEG 400, 1% 2-ME, RT, CRYSTALLIZED FROM FULL LENGTH APOE4 CONSTRUCT (299 RESIDUES). PROTEOLYTIC CLEAVAGE IN CRYSTALLIZATION DROP TO 22K FRAGMENT. NEW, THIRD ORTHOGONAL CRYSTAL FORM OF APOE (ORTHO-3)
Resolution 1.70 Å R-free 0.247
1H7I Apolipoprotein E3 22kD fragment LYS146GLN mutant Deposited 2001-07-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 19–209（191 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 1-191
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；50MM NA-CACODYLATE, PH 5.6, 20-25% PEG 400, 1% 2-ME. RT. ORTHORHOMBIC FORM ORTHO-2 APPEARS (SEE PDB ENTRY 1OR2).
Resolution 1.90 Å R-free 0.259
1LE2 STRUCTURAL BASIS FOR ALTERED FUNCTION IN THE COMMON MUTANTS OF HUMAN APOLIPOPROTEIN-E Deposited 1991-08-22 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 41–184（144 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
1LE4 STRUCTURAL BASIS FOR ALTERED FUNCTION IN THE COMMON MUTANTS OF HUMAN APOLIPOPROTEIN-E Deposited 1991-08-22 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 41–184（144 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
1LPE THREE-DIMENSIONAL STRUCTURE OF THE LDL RECEPTOR-BINDING DOMAIN OF HUMAN APOLIPOPROTEIN E Deposited 1991-08-22 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 41–184（144 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.25 Å
1NFN APOLIPOPROTEIN E3 (APOE3) Deposited 1996-07-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 19–209（191 aa） Fragment：22KD RECEPTOR BINDING DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å R-free 0.259
1NFO APOLIPOPROTEIN E2 (APOE2, D154A MUTATION) Deposited 1996-07-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 19–209（191 aa） Fragment：22KD RECEPTOR BINDING DOMAIN
Mutation：D154A No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å R-free 0.270
1OEF PEPTIDE OF HUMAN APOE RESIDUES 263-286, NMR, 5 STRUCTURES AT PH 4.8, 37 DEGREES CELSIUS AND PEPTIDE:SDS MOLE RATIO OF 1:90 Deposited 1996-03-16 Different construct 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 281–304（24 aa） Fragment：RESIDUES 263 - 286
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.8；310 K
Resolution not provided
1OEG PEPTIDE OF HUMAN APOE RESIDUES 267-289, NMR, 5 STRUCTURES AT PH 6.0, 37 DEGREES CELSIUS AND PEPTIDE:SDS MOLE RATIO OF 1:90 Deposited 1996-03-16 Different construct 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 285–307（23 aa） Fragment：RESIDUES 267 - 289
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；310 K
Resolution not provided
1OR2 APOLIPOPROTEIN E3 (APOE3) TRUNCATION MUTANT 165 Deposited 1999-03-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 19–183（165 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 1-165
Mutation：TRUNCATION AT RESIDUE 165 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, HANGING DROP；pH 5.6；293 K；50MM NA-CACODYLATE, PH 5.6, 10-20% PEG 400 AT ROOM TEMPERATURE. NO 2-ME ADDED. NOTE: WITH 2-ME OR LOWER PEG CONCENTRATIONS, OTHER CRYSTAL FORMS APPEARS (SEE PDB ENTRIES 1BZ4, 1OR3), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.297
1OR3 APOLIPOPROTEIN E3 (APOE3), TRIGONAL TRUNCATION MUTANT 165 Deposited 1998-12-01 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 19–183（165 aa） Fragment：RECEPTOR BINDING DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；RT, 50MM NA-CACODYLATE, PH 5.6, 10-20% PEG 400, 1% 2-ME. NOTE: W/O 2-ME OR HIGHER PEG CONCENTRATIONS, OTHER CRYSTAL FORMS APPEARS (SEE PDB ENTRIES 1BZ4, 1OR2).
Resolution 1.73 Å R-free 0.238
2KC3 NMR solution structure of complete receptor binding domain of human apolipoprotein E Deposited 2008-12-15 Different construct 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 19–201（183 aa） Fragment：UNP residues 19-201
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient
NMR sample composition 1 mM [U-100% 13C; U-100% 15N; U-70% 2H] Human apolipoprotein E N-terminal domain-1, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N; U-30% 2H] Human apolipoprotein E N-terminal domain-2, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2KNY Fusion construct of CR17 from LRP-1 and ApoE residues 130-149 Deposited 2009-09-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 147–167（21 aa） Fragment：Fusion of LRP UNP residues 2770-2817 and Apo-E UNP residues 147-167
Not recorded CA CALCIUM ION × 1 SOLUTION NMR
NMR measurement conditions pH 7.45；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient
NMR measurement conditions pH 7.45；298 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient
NMR sample composition 20 mM [U-99% 2H] HEPES-1, 50 mM sodium chloride-2, 3 mM sodium azide-3, 5 mM CALCIUM ION-4, 0.8 mM [U-99% 13C; U-99% 15N] entity_1-5, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 20 mM [U-99% 2H] HEPES-6, 50 mM sodium chloride-7, 3 mM sodium azide-8, 5 mM CALCIUM ION-9, 0.8 mM [U-99% 13C; U-99% 15N] entity_1-10, 100% D2O | 100% D2O
NMR sample composition 20 mM [U-99% 2H] HEPES-11, 50 mM sodium chloride-12, 3 mM sodium azide-13, 5 mM CALCIUM ION-14, 0.8 mM [U-99% 15N] entity_1-15, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 20 mM [U-99% 2H] HEPES-16, 150 mM sodium chloride-17, 3 mM sodium azide-18, 2 mM [U-99% 2H] EDTA-19, 0.5 mM [U-99% 15N] entity_2-20, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 20 mM [U-99% 2H] HEPES-21, 150 mM sodium chloride-22, 3 mM sodium azide-23, 2 mM [U-99% 2H] EDTA-24, 0.5 mM [U-99% 13C; U-99% 15N] entity_2-25, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2L7B NMR Structure of full length apoE3 Deposited 2010-12-07 Different construct 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 19–317（299 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.9；303 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient
NMR sample composition 1 mM [U-13C; U-15N; U-2H] apoE3, 100 mM sodium phosphate, 10 mM DTT, 5 mM [U-100% 2H] EDTA, 1 mM DSS, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N; U-50% 2H] apoE3, 10 mM DTT, 1 mM DSS, 5 mM [U-100% 2H] EDTA, 100 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6NCN Fragment-based Discovery of an apoE4 Stabilizer Deposited 2018-12-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 20–181（162 aa）
Not recorded KJM 1-(3-chlorophenyl)cyclobutane-1-carboximidamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；296 K；20% w/v Polyethylene glycol monomethyl ether mesylate 5,000; 0.1M Bis-Tris buffer at pH6.5
Resolution 1.82 Å R-free 0.219
6NCO Fragment-based Discovery of an apoE4 Stabilizer Deposited 2018-12-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 20–181（162 aa）
Not recorded KQP 1-[5-chloro-4'-(2-hydroxypropan-2-yl)[1,1'-biphenyl]-3-yl]cyclobutane-1-carboximidamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；296 K；20% w/v Polyethylene glycol monomethyl ether mesylate 5,000; 0.1M Bis-Tris buffer at pH6.5
Resolution 1.71 Å R-free 0.220
6V7M Crystal structure of a proteolytically cleaved, amino terminal domain of apolipoprotein E3 Deposited 2019-12-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–100（100 aa） Fragment：UNP residues 1-100
Chain B 101–183（83 aa） Fragment：UNP residues 101-183
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；298 K；Crystallization was by sitting drop vapor diffusion in Cryschem plates at room temperature. Reservoirs were 16% to 18 % 2-methyl-2,4-pentanediol (MPD) buffered with 0.1 M sodium acetate at pH 5.8 and including 0.25% octyl-beta-D-1-thioglucopyranoside. The droplets were initial composed of equal amounts of the reservoir and an 8 mg/ml solution of the protein in 0.02 M ammonium carbonate.
Resolution 2.00 Å R-free 0.260
7FCR Crystal structure of the N-terminal domain of mutants of Human Apolipoprotein-E (ApoE) Deposited 2021-07-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 19–209（191 aa）
Mutation：C130I NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 5.15；294 K；100 mM sodium cacodylate, 28% PEG 400
Resolution 1.40 Å R-free 0.194
7FCS Crystal structure of the N-terminal domain of mutants of Human Apolipoprotein-E (ApoE) Deposited 2021-07-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 19–209（191 aa）
Mutation：C130V NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 5.15；294 K；100 mM sodium cacodylate, 28% PEG 400
Resolution 1.60 Å R-free 0.216
7UVJ Rationally Designed ED1 Epitope-Scaffold Immunogen for SARS-CoV-2 Deposited 2022-05-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 40–183（144 aa）
Not recorded GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；0.2 M sodium formate, 20% w/v PEG3350
Resolution 1.99 Å R-free 0.312
7UVJ Rationally Designed ED1 Epitope-Scaffold Immunogen for SARS-CoV-2 Deposited 2022-05-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 40–183（144 aa）
Not recorded GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；0.2 M sodium formate, 20% w/v PEG3350
Resolution 1.99 Å R-free 0.312
8AX8 Human Apolipoprotein E4 (ApoE4) N-terminal domain (space group P3121) Deposited 2022-08-31 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 19–317（299 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；HEPES, PEG3350
Resolution 1.55 Å R-free 0.231
8AX9 Human Apolipoprotein E4 (ApoE4) N-terminal domain (space group P212121) Deposited 2022-08-31 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 19–317（299 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；HEPES, PEG3350
Resolution 1.55 Å R-free 0.195
8CDY N-terminal domain of human apolipoprotein E Deposited 2023-02-01 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 19–317（299 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；HEPES, PEG 6000
Resolution 1.90 Å R-free 0.231
8CE0 N-terminal domain of human apolipoprotein E Deposited 2023-02-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 19–317（299 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；NaCl, Hepes, PEG 8000
Resolution 1.75 Å R-free 0.215
8GRX APOE4 receptor in complex with APOE4 NTD Deposited 2022-09-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 41–180（140 aa）
Chain C 41–180（140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

28 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name APOE_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 10–155； UniProt 41–186 Author chain C； PDBConstruct 10–155； UniProt 41–186

Apoptosis regulator Bcl-2,Apoptosis regulator Bcl-2

Homo sapiens

UniProt P10415

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–34 Chain B； UniProt 92–207 Fragment：UNP residues 1-34,UNP residues 92-207 Apolipoprotein E × 1 （P02649） SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295.15 K；17% PEG2000, 0.1M Sodium Succinate (pH 5.5), 0.32M Ammonium Sulfate Resolution 2.50 Å R-free 0.275
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 1–34 Chain D； UniProt 92–207 Fragment：UNP residues 1-34,UNP residues 92-207 Apolipoprotein E × 1 （P02649） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295.15 K；17% PEG2000, 0.1M Sodium Succinate (pH 5.5), 0.32M Ammonium Sulfate Resolution 2.50 Å R-free 0.275

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 6IWB Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1G5M HUMAN BCL-2, ISOFORM 1 Deposited 2000-11-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–34（34 aa）
Chain A 92–207（116 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.8；298 K；Ionic strength (raw mmCIF value) 20 mM；Pressure ambient
NMR sample composition 15N-Bcl-2(1); 15N,13C-BCL-2(1) | H2O
NMR sample composition 15N,13C-Bcl-2(1) | D2O
Resolution not provided
1GJH HUMAN BCL-2, ISOFORM 2 Deposited 2001-05-31 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–34（34 aa）
Chain A 92–207（116 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.8；298 K；Ionic strength (raw mmCIF value) 20 mM；Pressure AMBIENT
NMR sample composition 15N-Bcl-2(2); 15N,13C-BCL-2(2) | H2O
NMR sample composition 15N, 13C-Bcl-2(2) | D2O
Resolution not provided
1YSW Solution structure of the anti-apoptotic protein Bcl-2 complexed with an acyl-sulfonamide-based ligand Deposited 2005-02-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–34（32 aa）
Chain A 91–205（115 aa）
Not recorded 43B 3-NITRO-N-{4-[2-(2-PHENYLETHYL)-1,3-BENZOTHIAZOL-5-YL]BENZOYL}-4-{[2-(PHENYLSULFANYL)ETHYL]AMINO}BENZENESULFONAMIDE × 1 SOLUTION NMR
NMR measurement conditions pH 8；298 K；Ionic strength (raw mmCIF value) 25 mM；Pressure ambient
NMR sample composition 1 mM Bcl-2 U-15N,13C, 25 mM Deuterated TRIS, 1 mM deuterated dithiothreitol, 100% D2O | 100% D2O
Resolution not provided
2O21 Solution structure of the anti-apoptotic protein Bcl-2 in complex with an acyl-sulfonamide-based ligand Deposited 2006-11-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–34（32 aa）
Chain A 92–207（116 aa）
Not recorded 43B 3-NITRO-N-{4-[2-(2-PHENYLETHYL)-1,3-BENZOTHIAZOL-5-YL]BENZOYL}-4-{[2-(PHENYLSULFANYL)ETHYL]AMINO}BENZENESULFONAMIDE × 1 SOLUTION NMR
NMR measurement conditions pH 8；298 K；Ionic strength (raw mmCIF value) 25 mM TRIS; 150 mM sodium chloride；Pressure 1
NMR sample composition 25mM TRIS buffer; 150 mM sodium chloride; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2O22 Solution structure of the anti-apoptotic protein Bcl-2 in complex with an acyl-sulfonamide-based ligand Deposited 2006-11-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–34（32 aa）
Chain A 92–207（116 aa）
Not recorded LIU N-[(4-{[1,1-dimethyl-2-(phenylthio)ethyl]amino}-3-nitrophenyl)sulfonyl]-4-(4,4-dimethylpiperidin-1-yl)benzamide × 1 SOLUTION NMR
NMR measurement conditions pH 8；298 K；Ionic strength (raw mmCIF value) 25 mM TRIS; 150 mM sodium chloride；Pressure 1
NMR sample composition 25 mM TRIS buffer; 150 mM sodium chloride; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2O2F Solution structure of the anti-apoptotic protein Bcl-2 in complex with an acyl-sulfonamide-based ligand Deposited 2006-11-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 8–31（24 aa）
Chain A 92–204（113 aa）
Not recorded LI0 4-(4-BENZYL-4-METHOXYPIPERIDIN-1-YL)-N-[(4-{[1,1-DIMETHYL-2-(PHENYLTHIO)ETHYL]AMINO}-3-NITROPHENYL)SULFONYL]BENZAMIDE × 1 SOLUTION NMR
NMR measurement conditions pH 8；298 K；Ionic strength (raw mmCIF value) 25 mM TRIS; 150 mM sodium chloride；Pressure 1
NMR sample composition 25mM TRIS buffer; 150 mM sodium chloride; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2W3L Crystal Structure of Chimaeric Bcl2-xL and Phenyl Tetrahydroisoquinoline Amide Complex Deposited 2008-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 9–33（25 aa） Fragment：RESIDUES 9-33,92-206
Chain A 92–206（115 aa） Fragment：RESIDUES 9-33,92-206
Not recorded DRO 1-(2-{[(3S)-3-(aminomethyl)-3,4-dihydroisoquinolin-2(1H)-yl]carbonyl}phenyl)-4-chloro-5-methyl-N,N-diphenyl-1H-pyrazole-3-carboxamide × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å R-free 0.258
2W3L Crystal Structure of Chimaeric Bcl2-xL and Phenyl Tetrahydroisoquinoline Amide Complex Deposited 2008-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 9–33（25 aa） Fragment：RESIDUES 9-33,92-206
Chain B 92–206（115 aa） Fragment：RESIDUES 9-33,92-206
Not recorded DRO 1-(2-{[(3S)-3-(aminomethyl)-3,4-dihydroisoquinolin-2(1H)-yl]carbonyl}phenyl)-4-chloro-5-methyl-N,N-diphenyl-1H-pyrazole-3-carboxamide × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å R-free 0.258
2XA0 Crystal structure of BCL-2 in complex with a BAX BH3 peptide Deposited 2010-03-25 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–207（207 aa） Fragment：RESIDUES 1-207
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M SODIUM ACETATE (PH 4.2), 3.0 M SODIUM FORMATE
Resolution 2.70 Å R-free 0.242
2XA0 Crystal structure of BCL-2 in complex with a BAX BH3 peptide Deposited 2010-03-25 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–207（207 aa） Fragment：RESIDUES 1-207
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M SODIUM ACETATE (PH 4.2), 3.0 M SODIUM FORMATE
Resolution 2.70 Å R-free 0.242
4AQ3 HUMAN BCL-2 WITH PHENYLACYLSULFONAMIDE INHIBITOR Deposited 2012-04-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–33（33 aa） Fragment：RESIDUES 1-33 AND 92-207 OF P10415 AND RESIDUES 29-44 OF Q07817
Chain A 92–207（116 aa） Fragment：RESIDUES 1-33 AND 92-207 OF P10415 AND RESIDUES 29-44 OF Q07817
Not recorded 398 N,N-dibutyl-4-chloranyl-1-[2-(3,4-dihydro-1H-isoquinolin-2-ylcarbonyl)-4-[(7-iodanylnaphthalen-2-yl)sulfonylcarbamoyl]phenyl]-5-methyl-pyrazole-3-carboxamide × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å R-free 0.245
4AQ3 HUMAN BCL-2 WITH PHENYLACYLSULFONAMIDE INHIBITOR Deposited 2012-04-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–33（33 aa） Fragment：RESIDUES 1-33 AND 92-207 OF P10415 AND RESIDUES 29-44 OF Q07817
Chain B 92–207（116 aa） Fragment：RESIDUES 1-33 AND 92-207 OF P10415 AND RESIDUES 29-44 OF Q07817
Not recorded 398 N,N-dibutyl-4-chloranyl-1-[2-(3,4-dihydro-1H-isoquinolin-2-ylcarbonyl)-4-[(7-iodanylnaphthalen-2-yl)sulfonylcarbamoyl]phenyl]-5-methyl-pyrazole-3-carboxamide × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å R-free 0.245
4AQ3 HUMAN BCL-2 WITH PHENYLACYLSULFONAMIDE INHIBITOR Deposited 2012-04-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–33（33 aa） Fragment：RESIDUES 1-33 AND 92-207 OF P10415 AND RESIDUES 29-44 OF Q07817
Chain C 92–207（116 aa） Fragment：RESIDUES 1-33 AND 92-207 OF P10415 AND RESIDUES 29-44 OF Q07817
Not recorded 398 N,N-dibutyl-4-chloranyl-1-[2-(3,4-dihydro-1H-isoquinolin-2-ylcarbonyl)-4-[(7-iodanylnaphthalen-2-yl)sulfonylcarbamoyl]phenyl]-5-methyl-pyrazole-3-carboxamide × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å R-free 0.245
4AQ3 HUMAN BCL-2 WITH PHENYLACYLSULFONAMIDE INHIBITOR Deposited 2012-04-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–33（33 aa） Fragment：RESIDUES 1-33 AND 92-207 OF P10415 AND RESIDUES 29-44 OF Q07817
Chain D 92–207（116 aa） Fragment：RESIDUES 1-33 AND 92-207 OF P10415 AND RESIDUES 29-44 OF Q07817
Not recorded 398 N,N-dibutyl-4-chloranyl-1-[2-(3,4-dihydro-1H-isoquinolin-2-ylcarbonyl)-4-[(7-iodanylnaphthalen-2-yl)sulfonylcarbamoyl]phenyl]-5-methyl-pyrazole-3-carboxamide × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å R-free 0.245
4AQ3 HUMAN BCL-2 WITH PHENYLACYLSULFONAMIDE INHIBITOR Deposited 2012-04-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain E 1–33（33 aa） Fragment：RESIDUES 1-33 AND 92-207 OF P10415 AND RESIDUES 29-44 OF Q07817
Chain E 92–207（116 aa） Fragment：RESIDUES 1-33 AND 92-207 OF P10415 AND RESIDUES 29-44 OF Q07817
Not recorded 398 N,N-dibutyl-4-chloranyl-1-[2-(3,4-dihydro-1H-isoquinolin-2-ylcarbonyl)-4-[(7-iodanylnaphthalen-2-yl)sulfonylcarbamoyl]phenyl]-5-methyl-pyrazole-3-carboxamide × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å R-free 0.245
4AQ3 HUMAN BCL-2 WITH PHENYLACYLSULFONAMIDE INHIBITOR Deposited 2012-04-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain F 1–33（33 aa） Fragment：RESIDUES 1-33 AND 92-207 OF P10415 AND RESIDUES 29-44 OF Q07817
Chain F 92–207（116 aa） Fragment：RESIDUES 1-33 AND 92-207 OF P10415 AND RESIDUES 29-44 OF Q07817
Not recorded 398 N,N-dibutyl-4-chloranyl-1-[2-(3,4-dihydro-1H-isoquinolin-2-ylcarbonyl)-4-[(7-iodanylnaphthalen-2-yl)sulfonylcarbamoyl]phenyl]-5-methyl-pyrazole-3-carboxamide × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å R-free 0.245
4IEH Crystal Structure of human Bcl-2 in complex with a small molecule inhibitor targeting Bcl-2 BH3 domain interactions Deposited 2012-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–34（34 aa） Fragment：SEE REMARK 999
Chain A 92–207（116 aa） Fragment：SEE REMARK 999
Not recorded 1E9 N-(6-{4-[(4'-chlorobiphenyl-2-yl)methyl]piperazin-1-yl}-1,1-dioxido-1,2-benzothiazol-3-yl)-4-{[(2R)-4-(dimethylamino)-1-(phenylsulfanyl)butan-2-yl]amino}-3-nitrobenzenesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.6；277 K；0.05 M succinic acid, 0.25 M sodium malonate, 12% PEG3350, 0.1 M Tris-HCl, pH 8.6, VAPOR DIFFUSION, temperature 277.0K
Resolution 2.10 Å R-free 0.218
4LVT Bcl_2-Navitoclax (ABT-263) Complex Deposited 2013-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–34（34 aa） Fragment：UNP RESIDUES 1-34, 92-207
Chain A 92–207（116 aa） Fragment：UNP RESIDUES 1-34, 92-207
Mutation：A2P Mutation：A2P 1XJ 4-(4-{[2-(4-chlorophenyl)-5,5-dimethylcyclohex-1-en-1-yl]methyl}piperazin-1-yl)-N-[(4-{[(2R)-4-(morpholin-4-yl)-1-(phenylsulfanyl)butan-2-yl]amino}-3-[(trifluoromethyl)sulfonyl]phenyl)sulfonyl]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.2；296 K；0.5 M (NH4)2SO4, 0.1 M Na Acetate, 0.2 M NaCl, pH 4.2, VAPOR DIFFUSION, temperature 296K
Resolution 2.05 Å R-free 0.222
4LVT Bcl_2-Navitoclax (ABT-263) Complex Deposited 2013-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–34（34 aa） Fragment：UNP RESIDUES 1-34, 92-207
Chain B 92–207（116 aa） Fragment：UNP RESIDUES 1-34, 92-207
Mutation：A2P Mutation：A2P 1XJ 4-(4-{[2-(4-chlorophenyl)-5,5-dimethylcyclohex-1-en-1-yl]methyl}piperazin-1-yl)-N-[(4-{[(2R)-4-(morpholin-4-yl)-1-(phenylsulfanyl)butan-2-yl]amino}-3-[(trifluoromethyl)sulfonyl]phenyl)sulfonyl]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.2；296 K；0.5 M (NH4)2SO4, 0.1 M Na Acetate, 0.2 M NaCl, pH 4.2, VAPOR DIFFUSION, temperature 296K
Resolution 2.05 Å R-free 0.222
4LXD Bcl_2-Navitoclax Analog (without Thiophenyl) Complex Deposited 2013-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–34（34 aa） Fragment：UNP RESIDUES 1-34, 92-207
Chain A 92–207（116 aa） Fragment：UNP RESIDUES 1-34, 92-207
Mutation：A2P Mutation：A2P 1XV 4-(4-{[4-(4-chlorophenyl)-5,6-dihydro-2H-pyran-3-yl]methyl}piperazin-1-yl)-N-{[3-nitro-4-(tetrahydro-2H-pyran-4-ylamino)phenyl]sulfonyl}benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；296 K；1.5 M (NH4)2SO4, 0.1 M MES, 8%(V/V) PEG400, pH 6.5, VAPOR DIFFUSION, temperature 296K
Resolution 1.90 Å R-free 0.212
4MAN Bcl_2-Navitoclax Analog (with Indole) Complex Deposited 2013-08-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–34（34 aa） Fragment：UNP RESIDUES 1-34, 92-207
Chain A 92–207（116 aa） Fragment：UNP RESIDUES 1-34, 92-207
Not recorded 1Y1 4-[4-({4'-chloro-3-[2-(dimethylamino)ethoxy]biphenyl-2-yl}methyl)piperazin-1-yl]-2-(1H-indol-5-yloxy)-N-({3-nitro-4-[(tetrahydro-2H-pyran-4-ylmethyl)amino]phenyl}sulfonyl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；296 K；1.5 M Li2SO4, 0.1 M Tris HCl, pH 8.5, VAPOR DIFFUSION, temperature 296K
Resolution 2.07 Å R-free 0.234
4MAN Bcl_2-Navitoclax Analog (with Indole) Complex Deposited 2013-08-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–34（34 aa） Fragment：UNP RESIDUES 1-34, 92-207
Chain B 92–207（116 aa） Fragment：UNP RESIDUES 1-34, 92-207
Not recorded 1Y1 4-[4-({4'-chloro-3-[2-(dimethylamino)ethoxy]biphenyl-2-yl}methyl)piperazin-1-yl]-2-(1H-indol-5-yloxy)-N-({3-nitro-4-[(tetrahydro-2H-pyran-4-ylmethyl)amino]phenyl}sulfonyl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；296 K；1.5 M Li2SO4, 0.1 M Tris HCl, pH 8.5, VAPOR DIFFUSION, temperature 296K
Resolution 2.07 Å R-free 0.234
5AGW Bcl-2 alpha beta-1 complex Deposited 2015-02-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–34（34 aa） Fragment：RESIDUES 1-34,29-44,92-207
Chain B 92–207（116 aa） Fragment：RESIDUES 1-34,29-44,92-207
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；0.02M CACL2, 0.1M MOPS PH7.0, 10% 2-PROPANOL
Resolution 2.69 Å R-free 0.272
5AGW Bcl-2 alpha beta-1 complex Deposited 2015-02-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–34（34 aa） Fragment：RESIDUES 1-34,29-44,92-207
Chain A 92–207（116 aa） Fragment：RESIDUES 1-34,29-44,92-207
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；0.02M CACL2, 0.1M MOPS PH7.0, 10% 2-PROPANOL
Resolution 2.69 Å R-free 0.272
5AGX Bcl-2 alpha beta-1 LINEAR complex Deposited 2015-02-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–34（34 aa） Fragment：RESIDUES 1-34,29-44,92-207
Chain A 92–207（116 aa） Fragment：RESIDUES 1-34,29-44,92-207
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；PH 7.0
Resolution 2.24 Å R-free 0.245
5AGX Bcl-2 alpha beta-1 LINEAR complex Deposited 2015-02-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–34（34 aa） Fragment：RESIDUES 1-34,29-44,92-207
Chain B 92–207（116 aa） Fragment：RESIDUES 1-34,29-44,92-207
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；PH 7.0
Resolution 2.24 Å R-free 0.245
5JSN Bcl2-inhibitor complex Deposited 2016-05-09 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–207（207 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；30% Jeffamine ED-2001, pH7.0/100 mM HEPES pH 7.0
Resolution 2.10 Å R-free 0.205
5JSN Bcl2-inhibitor complex Deposited 2016-05-09 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–207（207 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；30% Jeffamine ED-2001, pH7.0/100 mM HEPES pH 7.0
Resolution 2.10 Å R-free 0.205
5VAU Bcl-2 complex with Beclin 1 BH3 domain Deposited 2017-03-28 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–34（34 aa）
Chain A 92–207（116 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1M Bis-tris chloride, pH 5.5, ).2M ammonium acetate, 25% PEG 3350
Resolution 1.75 Å R-free 0.215
5VAU Bcl-2 complex with Beclin 1 BH3 domain Deposited 2017-03-28 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–34（34 aa）
Chain B 92–207（116 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1M Bis-tris chloride, pH 5.5, ).2M ammonium acetate, 25% PEG 3350
Resolution 1.75 Å R-free 0.215
5VAU Bcl-2 complex with Beclin 1 BH3 domain Deposited 2017-03-28 Different construct Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–34（34 aa）
Chain C 92–207（116 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1M Bis-tris chloride, pH 5.5, ).2M ammonium acetate, 25% PEG 3350
Resolution 1.75 Å R-free 0.215
5VAU Bcl-2 complex with Beclin 1 BH3 domain Deposited 2017-03-28 Different construct Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–34（34 aa）
Chain D 92–207（116 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1M Bis-tris chloride, pH 5.5, ).2M ammonium acetate, 25% PEG 3350
Resolution 1.75 Å R-free 0.215
5VAX Bcl-2 complex with Beclin 1 BH3 domain Deposited 2017-03-28 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–34（34 aa）
Chain A 92–207（116 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；bis-tris chloride, pH 4.5, 0.2M ammonium acetate, 25% PEG 3350
Resolution 2.00 Å R-free 0.243
5VAX Bcl-2 complex with Beclin 1 BH3 domain Deposited 2017-03-28 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–34（34 aa）
Chain B 92–207（116 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；bis-tris chloride, pH 4.5, 0.2M ammonium acetate, 25% PEG 3350
Resolution 2.00 Å R-free 0.243
5VAX Bcl-2 complex with Beclin 1 BH3 domain Deposited 2017-03-28 Different construct Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–34（34 aa）
Chain C 92–207（116 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；bis-tris chloride, pH 4.5, 0.2M ammonium acetate, 25% PEG 3350
Resolution 2.00 Å R-free 0.243
5VAX Bcl-2 complex with Beclin 1 BH3 domain Deposited 2017-03-28 Different construct Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–34（34 aa）
Chain D 92–207（116 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；bis-tris chloride, pH 4.5, 0.2M ammonium acetate, 25% PEG 3350
Resolution 2.00 Å R-free 0.243
5VAY Bcl-2 complex with Beclin 1 T108D BH3 domain Deposited 2017-03-28 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–34（34 aa）
Chain A 92–207（116 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M Tris, pH 6.5, 0.2M ammonium acetate, 25% PEG 3350
Resolution 1.80 Å R-free 0.228
5VAY Bcl-2 complex with Beclin 1 T108D BH3 domain Deposited 2017-03-28 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–34（34 aa）
Chain B 92–207（116 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M Tris, pH 6.5, 0.2M ammonium acetate, 25% PEG 3350
Resolution 1.80 Å R-free 0.228
5VAY Bcl-2 complex with Beclin 1 T108D BH3 domain Deposited 2017-03-28 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–34（34 aa）
Chain C 92–207（116 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M Tris, pH 6.5, 0.2M ammonium acetate, 25% PEG 3350
Resolution 1.80 Å R-free 0.228
5VAY Bcl-2 complex with Beclin 1 T108D BH3 domain Deposited 2017-03-28 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–34（34 aa）
Chain D 92–207（116 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M Tris, pH 6.5, 0.2M ammonium acetate, 25% PEG 3350
Resolution 1.80 Å R-free 0.228
6GL8 Crystal structure of Bcl-2 in complex with the novel orally active inhibitor S55746 Deposited 2018-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 9–33（25 aa）
Chain A 92–206（115 aa）
Mutation：;L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E ; Mutation：;L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E,L95K, Q99E ; F3Q ~{N}-(4-hydroxyphenyl)-3-[6-[[(3~{S})-3-(morpholin-4-ylmethyl)-3,4-dihydro-1~{H}-isoquinolin-2-yl]carbonyl]-1,3-benzodioxol-5-yl]-~{N}-phenyl-5,6,7,8-tetrahydroindolizine-1-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；284 K；0.1 M sodium acetate buffer pH 5.25, 20% Jeffamine600, 10% PEG3350
Resolution 1.40 Å R-free 0.194
6O0K crystal structure of BCL-2 with venetoclax Deposited 2019-02-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–34（34 aa）
Chain A 92–207（116 aa）
Not recorded LBM 4-{4-[(4'-chloro-5,5-dimethyl[3,4,5,6-tetrahydro[1,1'-biphenyl]]-2-yl)methyl]piperazin-1-yl}-N-[(3-nitro-4-{[(oxan-4-yl )methyl]amino}phenyl)sulfonyl]-2-[(1H-pyrrolo[2,3-b]pyridin-5-yl)oxy]benzamide × 1 2PE NONAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；5% PEG4K, 40%PEG400, 0.1M MES pH 6.0
Resolution 1.62 Å R-free 0.202
6O0L crystal structure of BCL-2 G101V mutation with venetoclax Deposited 2019-02-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–34（34 aa）
Chain A 92–207（116 aa）
Mutation：G101V,G101V,G101V Mutation：G101V,G101V,G101V LBM 4-{4-[(4'-chloro-5,5-dimethyl[3,4,5,6-tetrahydro[1,1'-biphenyl]]-2-yl)methyl]piperazin-1-yl}-N-[(3-nitro-4-{[(oxan-4-yl )methyl]amino}phenyl)sulfonyl]-2-[(1H-pyrrolo[2,3-b]pyridin-5-yl)oxy]benzamide × 1 PEG DI(HYDROXYETHYL)ETHER × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；4% PEG4K, 35% PEG400, 0.08M MES pH 6.0
Resolution 2.20 Å R-free 0.227
6O0L crystal structure of BCL-2 G101V mutation with venetoclax Deposited 2019-02-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–34（34 aa）
Chain C 92–207（116 aa）
Mutation：G101V,G101V,G101V Mutation：G101V,G101V,G101V LBM 4-{4-[(4'-chloro-5,5-dimethyl[3,4,5,6-tetrahydro[1,1'-biphenyl]]-2-yl)methyl]piperazin-1-yl}-N-[(3-nitro-4-{[(oxan-4-yl )methyl]amino}phenyl)sulfonyl]-2-[(1H-pyrrolo[2,3-b]pyridin-5-yl)oxy]benzamide × 1 PEG DI(HYDROXYETHYL)ETHER × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；4% PEG4K, 35% PEG400, 0.08M MES pH 6.0
Resolution 2.20 Å R-free 0.227
6O0M crystal structure of BCL-2 F104L mutation with venetoclax Deposited 2019-02-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–34（34 aa）
Chain A 92–207（116 aa）
Mutation：F104L,F104L,F104L Mutation：F104L,F104L,F104L LBM 4-{4-[(4'-chloro-5,5-dimethyl[3,4,5,6-tetrahydro[1,1'-biphenyl]]-2-yl)methyl]piperazin-1-yl}-N-[(3-nitro-4-{[(oxan-4-yl )methyl]amino}phenyl)sulfonyl]-2-[(1H-pyrrolo[2,3-b]pyridin-5-yl)oxy]benzamide × 1 PEG DI(HYDROXYETHYL)ETHER × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；5% PEG4K, 40% PEG400, 0.1M MES pH 6.0
Resolution 1.75 Å R-free 0.218
6O0O crystal structure of BCL-2 G101V mutation with S55746 Deposited 2019-02-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–34（34 aa）
Chain A 92–207（116 aa）
Mutation：G101V,G101V,G101V Mutation：G101V,G101V,G101V F3Q ~{N}-(4-hydroxyphenyl)-3-[6-[[(3~{S})-3-(morpholin-4-ylmethyl)-3,4-dihydro-1~{H}-isoquinolin-2-yl]carbonyl]-1,3-benzodioxol-5-yl]-~{N}-phenyl-5,6,7,8-tetrahydroindolizine-1-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5；291 K；0.1M NaCl 0.1M Succinic acid-NaOH pH5.0 10% PEG200
Resolution 2.00 Å R-free 0.267
6O0O crystal structure of BCL-2 G101V mutation with S55746 Deposited 2019-02-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–34（34 aa）
Chain C 92–207（116 aa）
Mutation：G101V,G101V,G101V Mutation：G101V,G101V,G101V F3Q ~{N}-(4-hydroxyphenyl)-3-[6-[[(3~{S})-3-(morpholin-4-ylmethyl)-3,4-dihydro-1~{H}-isoquinolin-2-yl]carbonyl]-1,3-benzodioxol-5-yl]-~{N}-phenyl-5,6,7,8-tetrahydroindolizine-1-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5；291 K；0.1M NaCl 0.1M Succinic acid-NaOH pH5.0 10% PEG200
Resolution 2.00 Å R-free 0.267
6O0P crystal structure of BCL-2 G101A mutation with venetoclax Deposited 2019-02-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–34（34 aa）
Chain A 92–207（116 aa）
Mutation：G101A,G101A,G101A Mutation：G101A,G101A,G101A LBM 4-{4-[(4'-chloro-5,5-dimethyl[3,4,5,6-tetrahydro[1,1'-biphenyl]]-2-yl)methyl]piperazin-1-yl}-N-[(3-nitro-4-{[(oxan-4-yl )methyl]amino}phenyl)sulfonyl]-2-[(1H-pyrrolo[2,3-b]pyridin-5-yl)oxy]benzamide × 1 PEG DI(HYDROXYETHYL)ETHER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；5% PEG4K, 40% PEG400, 0.1M MES pH 6.0
Resolution 1.80 Å R-free 0.232
6QG8 Structure of human Bcl-2 in complex with PUMA BH3 peptide Deposited 2019-01-10 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 10–33（24 aa）
Chain A 92–203（112 aa）
Mutation：H20S, L95Q, R106L, F124G, R127Y, G128A, R129S, P168V, L175A, T178A, E179T, R183D Mutation：H20S, L95Q, R106L, F124G, R127Y, G128A, R129S, P168V, L175A, T178A, E179T, R183D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；284 K；from 0.2M MgCl2, 25% PegMME 2k, 0.1M Na Acetate buffer pH 5.5
Resolution 1.90 Å R-free 0.216
6QGG Structure of human Bcl-2 in complex with analogue of ABT-737 Deposited 2019-01-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 10–33（24 aa）
Chain A 92–203（112 aa）
Mutation：H20S, L95Q, R106L, F124G, R127Y, G128A, R129S, P168V, L175A, T178A, E179T, R183D Mutation：H20S, L95Q, R106L, F124G, R127Y, G128A, R129S, P168V, L175A, T178A, E179T, R183D J1H [(3~{R})-3-[[4-[[4-[4-[[2-(4-chlorophenyl)phenyl]methyl]piperazin-1-yl]phenyl]carbonylsulfamoyl]-2-nitro-phenyl]amino]-4-phenylsulfanyl-butyl]-(2-hydroxy-2-oxoethyl)-dimethyl-azanium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；284 K；1.4M Na/K phosphate pH 5.6
Resolution 1.50 Å R-free 0.173
6QGH Structure of human Bcl-2 in complex with ABT-263 Deposited 2019-01-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 10–33（24 aa）
Chain A 92–203（112 aa）
Mutation：H20S, L95Q, R106L, F124G, R127Y, G128A, R129S, P168V, L175A, T178A, E179T, R183D Mutation：H20S, L95Q, R106L, F124G, R127Y, G128A, R129S, P168V, L175A, T178A, E179T, R183D 1XJ 4-(4-{[2-(4-chlorophenyl)-5,5-dimethylcyclohex-1-en-1-yl]methyl}piperazin-1-yl)-N-[(4-{[(2R)-4-(morpholin-4-yl)-1-(phenylsulfanyl)butan-2-yl]amino}-3-[(trifluoromethyl)sulfonyl]phenyl)sulfonyl]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；284 K；0.2 M NaCl, 25% PEG3350 and 0.1 M Bis-Tris buffer pH 5.5
Resolution 2.00 Å R-free 0.206
6QGJ Structure of human Bcl-2 in complex with fragment/ABT-263 hybrid Deposited 2019-01-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 10–33（24 aa）
Chain A 92–203（112 aa）
Mutation：H20S, L95Q, R106L, F124G, R127Y, G128A, R129S, P168V, L175A, T178A, E179T, R183D Mutation：H20S, L95Q, R106L, F124G, R127Y, G128A, R129S, P168V, L175A, T178A, E179T, R183D J1T 4-[4-[(1~{R})-1-(6-methoxy-1,3-benzodioxol-5-yl)-2-pyrrolidin-1-yl-ethyl]phenyl]-~{N}-[4-[[(2~{R})-4-morpholin-4-yl-1-phenylsulfanyl-butan-2-yl]amino]-3-(trifluoromethylsulfonyl)phenyl]sulfonyl-benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；284 K；0.15M KSCN, 20% PEG1500 and 0.1M Na acetate buffer pH 5.5
Resolution 1.90 Å R-free 0.225
6QGK Structure of human Bcl-2 in complex with THIQ-phenyl pyrazole compound Deposited 2019-01-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 10–33（24 aa）
Chain A 92–203（112 aa）
Mutation：H20S, E42A, E44A, L95Q, R106L, E114Q, F124G, R127Y, G128A, R129S, E135A, E165A, P168V, L175A, T178A, E179T, R183D Mutation：H20S, E42A, E44A, L95Q, R106L, E114Q, F124G, R127Y, G128A, R129S, E135A, E165A, P168V, L175A, T178A, E179T, R183D J1Q 1-[2-[[(3~{S})-3-(aminomethyl)-3,4-dihydro-1~{H}-isoquinolin-2-yl]carbonyl]phenyl]-~{N},~{N}-dibutyl-5-methyl-pyrazole-3-carboxamide × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；284 K；0.2M Ca Acetate, 15% PEG4k, 0.1M Tris buffer pH 7.5
Resolution 1.80 Å R-free 0.202
7LHB Crystal structure of Bcl-2 in complex with prodrug ABBV-167 Deposited 2021-01-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–34（34 aa） Fragment：UNP residues 35-91 replaced with DVEENRTEAPEGTESE
Chain A 92–207（116 aa） Fragment：UNP residues 35-91 replaced with DVEENRTEAPEGTESE
Mutation：A4P, R26K Mutation：A4P, R26K XZD Phosphoric acid mono-[5-(5-{4-[2-(4-chloro-phenyl)-4,4-dimethyl-cyclohex-1-enylmethyl]-piperazin-1-yl}-2-{3-nitro-4-[(tetrahydro-pyran-4-ylmethyl)-amino]-benzenesulfonylaminocarbonyl}-phenoxy)-pyrrolo[2,3-b]pyridin-7-ylmethyl] ester × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；20% w/v PEG4000, 0.1 M Tris-HCl, pH 8.0, 0.2 M calcium chloride
Resolution 2.07 Å R-free 0.238
7LHB Crystal structure of Bcl-2 in complex with prodrug ABBV-167 Deposited 2021-01-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–34（34 aa） Fragment：UNP residues 35-91 replaced with DVEENRTEAPEGTESE
Chain B 92–207（116 aa） Fragment：UNP residues 35-91 replaced with DVEENRTEAPEGTESE
Mutation：A4P, R26K Mutation：A4P, R26K XZD Phosphoric acid mono-[5-(5-{4-[2-(4-chloro-phenyl)-4,4-dimethyl-cyclohex-1-enylmethyl]-piperazin-1-yl}-2-{3-nitro-4-[(tetrahydro-pyran-4-ylmethyl)-amino]-benzenesulfonylaminocarbonyl}-phenoxy)-pyrrolo[2,3-b]pyridin-7-ylmethyl] ester × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；20% w/v PEG4000, 0.1 M Tris-HCl, pH 8.0, 0.2 M calcium chloride
Resolution 2.07 Å R-free 0.238
7LHB Crystal structure of Bcl-2 in complex with prodrug ABBV-167 Deposited 2021-01-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–34（34 aa） Fragment：UNP residues 35-91 replaced with DVEENRTEAPEGTESE
Chain C 92–207（116 aa） Fragment：UNP residues 35-91 replaced with DVEENRTEAPEGTESE
Mutation：A4P, R26K Mutation：A4P, R26K XZD Phosphoric acid mono-[5-(5-{4-[2-(4-chloro-phenyl)-4,4-dimethyl-cyclohex-1-enylmethyl]-piperazin-1-yl}-2-{3-nitro-4-[(tetrahydro-pyran-4-ylmethyl)-amino]-benzenesulfonylaminocarbonyl}-phenoxy)-pyrrolo[2,3-b]pyridin-7-ylmethyl] ester × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；20% w/v PEG4000, 0.1 M Tris-HCl, pH 8.0, 0.2 M calcium chloride
Resolution 2.07 Å R-free 0.238
7Y90 Crystal Structure Analysis of cp1 bound BCL2 Deposited 2022-06-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–34（34 aa）
Chain A 92–207（116 aa）
Not recorded JFF (2R)-3-[2-(aminomethyl)-3-azanyl-1-[4-[2-(2-chloranylethanoylamino)ethylcarbamoyl]phenyl]prop-1-enyl]sulfanyl-2-(carboxyamino)propanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1M Bis-Tris pH6.5, 2.0M Ammonium Sulfate
Resolution 2.09 Å R-free 0.276
7YA5 Crystal structure analysis of cp1 bound BCL2/G101V Deposited 2022-06-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–34（34 aa）
Chain A 92–207（116 aa）
Mutation：G101V Mutation：G101V JFF (2R)-3-[2-(aminomethyl)-3-azanyl-1-[4-[2-(2-chloranylethanoylamino)ethylcarbamoyl]phenyl]prop-1-enyl]sulfanyl-2-(carboxyamino)propanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Calcium acetate, PEG 3350
Resolution 1.85 Å R-free 0.243
7YB7 anti-apoptotic protein BCL-2-M12 Deposited 2022-06-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 10–35（26 aa）
Chain A 92–203（112 aa）
Not recorded IQ8 N-(2-acetamidoethyl)-4-(4,5-dihydro-1,3-thiazol-2-yl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；0.5 M Ammonium sulfate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 1.0 M Lithium sulfate monohydrate
Resolution 2.20 Å R-free 0.194
7YB7 anti-apoptotic protein BCL-2-M12 Deposited 2022-06-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 10–35（26 aa）
Chain B 92–203（112 aa）
Not recorded IQ8 N-(2-acetamidoethyl)-4-(4,5-dihydro-1,3-thiazol-2-yl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；0.5 M Ammonium sulfate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 1.0 M Lithium sulfate monohydrate
Resolution 2.20 Å R-free 0.194
8FY1 E3:PROTAC:target ternary complex structure (VCB/753b/BCL-2) Deposited 2023-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–207（207 aa）
Not recorded YF8 N-[8-(4-{[(1R,3R,4S)-4-(4-chlorophenyl)-1-methyl-3-{[4-(4-{[4-{[(2R)-4-(morpholin-4-yl)-1-(phenylsulfanyl)butan-2-yl]amino}-3-(trifluoromethanesulfonyl)benzene-1-sulfonyl]carbamoyl}phenyl)piperazin-1-yl]methyl}cyclohexyl]methyl}piperazin-1-yl)-8-oxooctanoyl]-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.1 M Tris-Cl pH 8.7, 18% PEG 8000, 0.2 M MgCl2 and 3% 1,6-Hexanediol
Resolution 2.56 Å R-free 0.250
8FY2 E3:PROTAC:target ternary complex structure (VCB/WH244/BCL-2) Deposited 2023-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–207（207 aa）
Not recorded YFH N-({4-[2-(4-{[(4R)-4'-chloro-4-methyl-6-{[4-(4-{[4-{[(2R)-4-[(1R,4R)-2-oxa-5-azabicyclo[2.2.1]heptan-5-yl]-1-(phenylsulfanyl)butan-2-yl]amino}-3-(trifluoromethanesulfonyl)benzene-1-sulfonyl]carbamoyl}phenyl)piperazin-1-yl]methyl}-2,3,4,5-tetrahydro[1,1'-biphenyl]-4-yl]methyl}piperazin-1-yl)-2-oxoethyl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4S)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.1 M Tris-Cl pH 8.7, 18% PEG 8000, 0.2 M MgCl2 and 3% 1,6-Hexanediol
Resolution 2.98 Å R-free 0.279
8HLL Crystal structure of p53/BCL2 fusion complex (complex 1) Deposited 2022-11-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 10–35（26 aa）
Chain B 92–203（112 aa）
Mutation：H20S,L95Q,R106L,F124G,R127Y,G128A,R129S,P168V,L175A,T178A,E179T,R183D Mutation：H20S,L95Q,R106L,F124G,R127Y,G128A,R129S,P168V,L175A,T178A,E179T,R183D ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；PEG 8K 8%-13%, 0.1M HEPES, 0.8% ethylene glycol
Resolution 2.62 Å R-free 0.280
8HLM Crystal structure of p53/BCL2 fusion complex (complex 2) Deposited 2022-11-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 10–35（26 aa）
Chain B 92–203（112 aa）
Mutation：H20S,L95Q,R106L,F124G,R127Y,G128A,R129S,P168V,L175A,T178A,E179T,R183D Mutation：H20S,L95Q,R106L,F124G,R127Y,G128A,R129S,P168V,L175A,T178A,E179T,R183D ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；0.1 M Imidazole, PEG8K 15-21%
Resolution 2.52 Å R-free 0.290
8HLN Crystal structure of p53/BCL2 fusion complex(complex3) Deposited 2022-11-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 10–35（26 aa）
Chain B 92–203（112 aa）
Mutation：H20S,L95Q,R106L,F124G,R127Y,G128A,R129S,P168V,L175A,T178A,E179T,R183D Mutation：H20S,L95Q,R106L,F124G,R127Y,G128A,R129S,P168V,L175A,T178A,E179T,R183D ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；0.1 M HEPES, PEG8000 8%-13%, 0.8% ethylene glycol
Resolution 2.35 Å R-free 0.253
8U27 Bcl-2-xL complexed with compound 35 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–34（34 aa）
Chain A 92–218（127 aa）
Not recorded ULL propan-2-yl {4-[(5S)-1-(4-bromobenzoyl)-5-phenyl-4,5-dihydro-1H-pyrazol-3-yl]phenyl}carbamate × 1 SOLUTION NMR
NMR measurement conditions pH 7.3；293 K；Ionic strength (raw mmCIF value) 0.0375；Pressure 1
NMR measurement conditions pH 7.3；293 K；Ionic strength (raw mmCIF value) 0.0375；Pressure 1
NMR measurement conditions pH 7.3；293 K；Ionic strength (raw mmCIF value) 0.0375；Pressure 1
NMR sample composition 300 uM [U-99% 13C; U-99% 15N] Bcl-2-xL, 300 uM Compound 35, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 300 uM [U-99% 15N] Bcl-2-xL, 300 uM Compound 35, 100% D2O | 100% D2O
NMR sample composition 300 uM [U-10% 13C] Bcl-2-xL, 300 uM Compound 35, 93% H2O/7% D2O | 93% H2O/7% D2O
Resolution not provided
8VWX Human Bcl-2 (G101V Mutant)/Bcl-xL Chimera Fused to Maltose-Binding Protein Deposited 2024-02-02 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 10–34（25 aa）
Chain A 92–207（116 aa）
Mutation：G101V Mutation：G101V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；100 mM Tris (pH 8.5), 25% PEG 3350, and 200 mM sodium chloride
Resolution 1.77 Å R-free 0.225
8VWZ Human Bcl-2 (G101V Mutant)/Bcl-xL Chimera Fused to MBP in Complex with Inhibitor S55746 Deposited 2024-02-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 10–34（25 aa）
Chain A 92–207（116 aa）
Mutation：G101V Mutation：G101V F3Q ~{N}-(4-hydroxyphenyl)-3-[6-[[(3~{S})-3-(morpholin-4-ylmethyl)-3,4-dihydro-1~{H}-isoquinolin-2-yl]carbonyl]-1,3-benzodioxol-5-yl]-~{N}-phenyl-5,6,7,8-tetrahydroindolizine-1-carboxamide × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；100 mM bis-tris (pH 5.5), 2 M ammonium sulfate
Resolution 2.33 Å R-free 0.256
8VXM Human Bcl-2/Bcl-xL Chimera Fused to MBP in Complex with Inhibitor S55746 Deposited 2024-02-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 10–34（25 aa）
Chain A 92–207（116 aa）
Not recorded F3Q ~{N}-(4-hydroxyphenyl)-3-[6-[[(3~{S})-3-(morpholin-4-ylmethyl)-3,4-dihydro-1~{H}-isoquinolin-2-yl]carbonyl]-1,3-benzodioxol-5-yl]-~{N}-phenyl-5,6,7,8-tetrahydroindolizine-1-carboxamide × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；100 mM Tris (pH 8.5), 25% PEG 3350, 200 mM lithium sulfate
Resolution 2.10 Å R-free 0.243
8VXN Human Bcl-2/Bcl-xL Chimera Fused to Maltose-Binding Protein Deposited 2024-02-05 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 10–34（25 aa）
Chain A 92–207（116 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；100 mM Tris (pH 8.0), 29% PEG 3350, 200 mM sodium chloride
Resolution 2.09 Å R-free 0.264
9O14 Crystal Structure of BCL-2 in complex with a stapled BAD BH3 peptide BAD SAHB 4.2 Deposited 2025-04-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–34（34 aa）
Chain A 92–207（116 aa）
Not recorded NI NICKEL (II) ION × 2 NTA NITRILOTRIACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；15.0% PEG-3350 and 150 mM CsCl
Resolution 1.73 Å R-free 0.222
9O15 Crystal Structure of BCL-2 (G101V) mutant in complex with a stapled BAD BH3 peptide BAD SAHB 4.2 Deposited 2025-04-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–34（34 aa）
Chain A 92–207（116 aa）
Mutation：G101V Mutation：G101V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；30% Tacsimate, pH 7.0
Resolution 1.99 Å R-free 0.223
9O15 Crystal Structure of BCL-2 (G101V) mutant in complex with a stapled BAD BH3 peptide BAD SAHB 4.2 Deposited 2025-04-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–34（34 aa）
Chain C 92–207（116 aa）
Mutation：G101V Mutation：G101V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；30% Tacsimate, pH 7.0
Resolution 1.99 Å R-free 0.223
9O15 Crystal Structure of BCL-2 (G101V) mutant in complex with a stapled BAD BH3 peptide BAD SAHB 4.2 Deposited 2025-04-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–34（34 aa）
Chain E 92–207（116 aa）
Mutation：G101V Mutation：G101V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；30% Tacsimate, pH 7.0
Resolution 1.99 Å R-free 0.223
9O15 Crystal Structure of BCL-2 (G101V) mutant in complex with a stapled BAD BH3 peptide BAD SAHB 4.2 Deposited 2025-04-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–34（34 aa）
Chain G 92–207（116 aa）
Mutation：G101V Mutation：G101V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；30% Tacsimate, pH 7.0
Resolution 1.99 Å R-free 0.223
9O15 Crystal Structure of BCL-2 (G101V) mutant in complex with a stapled BAD BH3 peptide BAD SAHB 4.2 Deposited 2025-04-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 5 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 1–34（34 aa）
Chain I 92–207（116 aa）
Mutation：G101V Mutation：G101V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；30% Tacsimate, pH 7.0
Resolution 1.99 Å R-free 0.223
9O15 Crystal Structure of BCL-2 (G101V) mutant in complex with a stapled BAD BH3 peptide BAD SAHB 4.2 Deposited 2025-04-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 6 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain K 1–34（34 aa）
Chain K 92–207（116 aa）
Mutation：G101V Mutation：G101V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；30% Tacsimate, pH 7.0
Resolution 1.99 Å R-free 0.223
9O16 Crystal Structure of human BCL-2 (R129L) mutant in complex with a stapled BAD BH3 peptide BAD SAHB 4.2 Deposited 2025-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–34（34 aa）
Chain A 92–207（116 aa）
Mutation：R129L Mutation：R129L IMD IMIDAZOLE × 2 SO4 SULFATE ION × 1 NI NICKEL (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG-3350, 200 mM Ammonium sulfate, 100 mM Tris, pH 8.5
Resolution 1.73 Å R-free 0.210

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

View Construct and Data Evidence
UniProt name BCL2_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–34； UniProt 1–34 Author chain B； PDBConstruct 51–166； UniProt 92–207 Author chain D； PDBConstruct 1–34； UniProt 1–34 Author chain D； PDBConstruct 51–166； UniProt 92–207

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

SAXS scattering curve SAXS Profile

SAXS profile for 6iwb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6iwb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6iwb
Deposition date deposition_date2018-12-05
Structure title titleCrystal structure of a computationally designed protein (LD3) in complex with BCL-2
Keywords keywordsAPOPTOSIS; APOPTOSIS
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier26.78 Å
Radius of gyration Rg (electron density) rg_electron25.87 Å
Forward intensity I(0) i067160100.00
Molecular weight molecular_weight63201.0 kDa
Excluded volume excluded_volume78684 ų
Envelope volume envelope_volume97428 ų
Hydration-shell volume shell_volume30858 ų
Envelope diameter envelope_diameter85.9 Å
Shell Rg shell_rg33.83 Å
Envelope Rg envelope_rg26.02 Å
Shape Rg shape_rg25.90 Å
Total Rg total_rg26.62 Å
Total atoms total_atoms4454
Residues n_residues563
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax86.4 Å
Rg (real space) rg_real26.72 Å
Rg uncertainty (real space) rg_real_error0.50 Å
I(0) (real space) i0_real6.7160e+07
I(0) uncertainty (real space) i0_real_error9.6980e+05
Rg (reciprocal space) rg_reciprocal26.74 Å
I(0) (reciprocal space) i0_reciprocal67160000.0000
Solution quality estimate total_estimate0.8975
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary32.2 Å
Skewness Skewness skewness0.282
Kurtosis Kurtosis kurtosis-0.421
Angular range angular_range— – 0.2950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha27450000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.976
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6iwbA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily20 — Apolipoprotein
Domain ID domain_id6iwbC00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily20 — Apolipoprotein
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8. Citations (1)

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9. Files and Curves (10)