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5vau

Bcl-2 complex with Beclin 1 BH3 domain

Method: X-RAY DIFFRACTION Dmax: 117.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera

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 A； UniProt 1–34 Chain A； UniProt 92–207 Not recorded Beclin-1 × 1 （Q14457） 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–34 Chain B； UniProt 92–207 Not recorded Beclin-1 × 1 （Q14457） 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
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 1–34 Chain C； UniProt 92–207 Not recorded Beclin-1 × 1 （Q14457） 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
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 1–34 Chain D； UniProt 92–207 Not recorded Beclin-1 × 1 （Q14457） 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

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 5VAU 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 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 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
5VAX Bcl-2 complex with Beclin 1 BH3 domain Deposited 2017-03-28 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 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 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 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 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 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 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 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
6IWB Crystal structure of a computationally designed protein (LD3) in complex with BCL-2 Deposited 2018-12-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–34（34 aa） Fragment：UNP residues 1-34,UNP residues 92-207
Chain B 92–207（116 aa） Fragment：UNP residues 1-34,UNP residues 92-207
Not recorded 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
6IWB Crystal structure of a computationally designed protein (LD3) in complex with BCL-2 Deposited 2018-12-05 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–34（34 aa） Fragment：UNP residues 1-34,UNP residues 92-207
Chain D 92–207（116 aa） Fragment：UNP residues 1-34,UNP residues 92-207
Not recorded No recorded non-water small molecule 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
6O0K crystal structure of BCL-2 with venetoclax Deposited 2019-02-16 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 76 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BCL2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–36； UniProt 1–34 Author chain A； PDBConstruct 53–168； UniProt 92–207 Author chain B； PDBConstruct 3–36； UniProt 1–34 Author chain B； PDBConstruct 53–168； UniProt 92–207 Author chain C； PDBConstruct 3–36； UniProt 1–34 Author chain C； PDBConstruct 53–168； UniProt 92–207 Author chain D； PDBConstruct 3–36； UniProt 1–34 Author chain D； PDBConstruct 53–168； UniProt 92–207

Beclin-1

OrganismNot specified

UniProt Q14457

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 E； UniProt 105–130 Not recorded Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera × 1 （P10415） 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain F； UniProt 105–130 Not recorded Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera × 1 （P10415） 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
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain G； UniProt 105–130 Not recorded Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera × 1 （P10415） 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
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain H； UniProt 105–130 Not recorded Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera × 1 （P10415） 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

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 5VAU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
13BV Cryo-EM structure of human PI3KC3-C1 complex Deposited 2026-04-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–450（450 aa）
Not recorded MYR MYRISTIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.77 Å
2P1L Structure of the Bcl-XL:Beclin 1 complex Deposited 2007-03-05 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 107–135（29 aa） Fragment：Beclin 1
Mutation：BH3 domain (residues 107-135) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；24% (w/v) PEG-400, 0.1M HEPES pH7.5, 0.2M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.262
2P1L Structure of the Bcl-XL:Beclin 1 complex Deposited 2007-03-05 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 107–135（29 aa） Fragment：Beclin 1
Mutation：BH3 domain (residues 107-135) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；24% (w/v) PEG-400, 0.1M HEPES pH7.5, 0.2M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.262
2P1L Structure of the Bcl-XL:Beclin 1 complex Deposited 2007-03-05 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 107–135（29 aa） Fragment：Beclin 1
Mutation：BH3 domain (residues 107-135) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；24% (w/v) PEG-400, 0.1M HEPES pH7.5, 0.2M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.262
2P1L Structure of the Bcl-XL:Beclin 1 complex Deposited 2007-03-05 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 107–135（29 aa） Fragment：Beclin 1
Mutation：BH3 domain (residues 107-135) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；24% (w/v) PEG-400, 0.1M HEPES pH7.5, 0.2M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.262
2P1L Structure of the Bcl-XL:Beclin 1 complex Deposited 2007-03-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain B 107–135（29 aa） Fragment：Beclin 1
Chain D 107–135（29 aa） Fragment：Beclin 1
Chain F 107–135（29 aa） Fragment：Beclin 1
Chain H 107–135（29 aa） Fragment：Beclin 1
Mutation：BH3 domain (residues 107-135) Mutation：BH3 domain (residues 107-135) Mutation：BH3 domain (residues 107-135) Mutation：BH3 domain (residues 107-135) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；24% (w/v) PEG-400, 0.1M HEPES pH7.5, 0.2M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.262
2P1L Structure of the Bcl-XL:Beclin 1 complex Deposited 2007-03-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 107–135（29 aa） Fragment：Beclin 1
Chain H 107–135（29 aa） Fragment：Beclin 1
Mutation：BH3 domain (residues 107-135) Mutation：BH3 domain (residues 107-135) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；24% (w/v) PEG-400, 0.1M HEPES pH7.5, 0.2M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.262
2P1L Structure of the Bcl-XL:Beclin 1 complex Deposited 2007-03-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 107–135（29 aa） Fragment：Beclin 1
Chain D 107–135（29 aa） Fragment：Beclin 1
Mutation：BH3 domain (residues 107-135) Mutation：BH3 domain (residues 107-135) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；24% (w/v) PEG-400, 0.1M HEPES pH7.5, 0.2M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.262
2PON Solution structure of the Bcl-xL/Beclin-1 complex Deposited 2007-04-27 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–23（23 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 50mM potassium phosphate；Pressure 1
NMR sample composition 1.5mM unlabelled Bcl-xL/Beclin-1 complex in 99.9% D2O; 50mM potassium phosphate | 99.9% D2O
NMR sample composition 1.5mM uniformly 15N labelled Bcl-xL/Beclin-1 complex in 90% H2O/10% D2O; 50mM potassium phosphate | 90% H2O/10% D2O
NMR sample composition 1.5mM uniformly 15N/13C labelled Bcl-xL/Beclin-1 complex in 99.9% D2O; 50mM potassium phosphate | 99.9% D2O
NMR sample composition 1.5mM 80% deuterated, uniformly 15N/13C labelled Bcl-xL/Beclin-1 complex in 90% H2O/10% D2O; 50mM potassium phosphate | 90% H2O/10% D2O
NMR sample composition 1.5mM 100% deuterated, uniformly 15N labelled Bcl-xL/Beclin-1 complex in 90% H2O/10% D2O; 50mM potassium phosphate | 90% H2O/10% D2O
Resolution not provided
3DVU Crystal structure of the complex of murine gamma-herpesvirus 68 Bcl-2 homolog M11 and the Beclin 1 BH3 domain Deposited 2008-07-20 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 105–130（26 aa） Fragment：BH3 domain, residues 105-130
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；20% PEG 3350, 0.1M sodium acetate, pH 4.5, 10mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.261
3DVU Crystal structure of the complex of murine gamma-herpesvirus 68 Bcl-2 homolog M11 and the Beclin 1 BH3 domain Deposited 2008-07-20 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 105–130（26 aa） Fragment：BH3 domain, residues 105-130
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；20% PEG 3350, 0.1M sodium acetate, pH 4.5, 10mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.261
4DDP crystal structure of Beclin 1 evolutionarily conserved domain(ECD) Deposited 2012-01-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 241–450（210 aa） Fragment：UNP residues 241-450
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；30% PEG 3350, 0.3M NaCl, 0.1M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.55 Å R-free 0.203
4MI8 Crystal structure of the complex of murine gamma-herpesvirus 68 Bcl-2 homolog M11 and a Beclin 1 BH3 domain-derived peptide Deposited 2013-08-30 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 C 107–130（24 aa） Fragment：UNP residues 107-130
Mutation：G120E, D121A SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；2.5 M ammonium sulfate, 8% 2-propanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.224
4MI8 Crystal structure of the complex of murine gamma-herpesvirus 68 Bcl-2 homolog M11 and a Beclin 1 BH3 domain-derived peptide Deposited 2013-08-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 107–130（24 aa） Fragment：UNP residues 107-130
Mutation：G120E, D121A SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；2.5 M ammonium sulfate, 8% 2-propanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.224
4MI8 Crystal structure of the complex of murine gamma-herpesvirus 68 Bcl-2 homolog M11 and a Beclin 1 BH3 domain-derived peptide Deposited 2013-08-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 107–130（24 aa） Fragment：UNP residues 107-130
Chain D 107–130（24 aa） Fragment：UNP residues 107-130
Mutation：G120E, D121A Mutation：G120E, D121A SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；2.5 M ammonium sulfate, 8% 2-propanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.224
5EFM Beclin 1 Flexible-helical Domian (FHD) (141-171) Deposited 2015-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 141–171（31 aa）
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.6；293 K；250mM potassium sodium tartrate tetrahydrate, 2.2 M ammonium sulfate, 100mM sodium citrate tribasic dihydrate (pH 5.6)
Resolution 1.95 Å R-free 0.216
5HHE Human Beclin 1 coiled-coil domain Deposited 2016-01-10 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain D 175–265（91 aa） Fragment：UNP entries 175-265
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7.5；293 K；39% 2-methyl-2, 4-pentadiol, 9% PEG400 and 100 mM Tris buffer, pH 7.5.
Resolution 1.46 Å R-free 0.208
5HHE Human Beclin 1 coiled-coil domain Deposited 2016-01-10 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 175–265（91 aa） Fragment：UNP entries 175-265
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7.5；293 K；39% 2-methyl-2, 4-pentadiol, 9% PEG400 and 100 mM Tris buffer, pH 7.5.
Resolution 1.46 Å R-free 0.208
5VAX Bcl-2 complex with Beclin 1 BH3 domain Deposited 2017-03-28 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 105–130（26 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 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 mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 105–130（26 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 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 mutation/modification Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 105–130（26 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 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 mutation/modification Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 105–130（26 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 105–130（26 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 105–130（26 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 105–130（26 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 105–130（26 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
6DCN Bcl-xL complex with Beclin 1 BH3 domain T108pThr Deposited 2018-05-07 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 105–130（26 aa）
Chain D 105–130（26 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2M NaCl, 10% glycerol
Resolution 2.44 Å R-free 0.229
6DCN Bcl-xL complex with Beclin 1 BH3 domain T108pThr Deposited 2018-05-07 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 105–130（26 aa）
Chain D 105–130（26 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2M NaCl, 10% glycerol
Resolution 2.44 Å R-free 0.229
6DCO Bcl-xL complex with Beclin 1 BH3 domain T108D Deposited 2018-05-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 105–130（26 aa）
Chain D 105–130（26 aa）
Mutation：T108D Mutation：T108D CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1M Tris pH 7.0, 0.2M MgCl2, 2.5M NaCl
Resolution 2.20 Å R-free 0.231
6HOI Structure of Beclin1 LIR motif bound to GABARAPL1 Deposited 2018-09-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 93–102（10 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M sodium acetate, 0.1M Hepes pH 7.5, 12% PEG 4000
Resolution 1.14 Å R-free 0.166
6HOI Structure of Beclin1 LIR motif bound to GABARAPL1 Deposited 2018-09-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 93–102（10 aa）
Not recorded ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M sodium acetate, 0.1M Hepes pH 7.5, 12% PEG 4000
Resolution 1.14 Å R-free 0.166
6HOJ Structure of Beclin1 LIR motif bound to GABARAP Deposited 2018-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 93–105（13 aa）
Chain B 93–105（13 aa）
Chain C 93–105（13 aa）
Not recorded SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；15% PEG 4000, 50 mM Bicine pH 8.8
Resolution 1.51 Å R-free 0.211
6HOK Structure of Beclin1 LIR (S96E) motif bound to GABARAP Deposited 2018-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 93–105（13 aa）
Not recorded EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.6 M ammonium sulfate, 100 mM TRIS pH 8.5, 10 % Glycerol
Resolution 1.61 Å R-free 0.198
7BL1 human complex II-BATS bound to membrane-attached Rab5a-GTP Deposited 2021-01-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain EEE 1–450（450 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Blot force 20, blot time 6 s
Resolution 9.80 Å
9C82 Structure of human ULK1C:PI3KC3-C1 supercomplex Deposited 2024-06-11 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–450（450 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；added 0.05% (w/v) octylglucopyranoside as surfactant
Resolution 6.84 Å
9MHF Cryo-EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L) Deposited 2024-12-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–450（450 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 MYR MYRISTIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.73 Å
9MHG Cryo EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L), VPS34 kinase domain in the inactive conformation Deposited 2024-12-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–450（450 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 MYR MYRISTIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；OG supplemented at time of grid preparation 0.05%
cryo-EM vitrification conditions Cryogen ETHANE；100% humidity, 3 s wait time, blot force -15
Resolution 3.20 Å
9MHH PI3KC3-C1 in complex with RAB1A. VPS34 kinase domain active conformation Deposited 2024-12-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–450（450 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；OG supplemented at time of grid preparation 0.05%
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
9RX5 VPS34-CII (VPS34 199-REIE-202 to 199-AAAA-202 mutant) bound to RAB5A (Q79L) Deposited 2025-07-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–450（450 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.15 Å
9RX6 VPS34-CII (VPS34 199-REIE-202 to 199-ERIR-202 mutant) bound to RAB5A (Q79L) on the VPS15 subunit Deposited 2025-07-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–450（450 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.52 Å
9RX8 Apo VPS34-CII (VPS34/VPS15/BECLIN1/UVRAG) Deposited 2025-07-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–450（450 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.87 Å
9RX9 VPS34-CII bound to RAB5A-GTP 1-212 (C19S, C63S, Q79L) on the VPS34 subunit Deposited 2025-07-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–450（450 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.99 Å
9RXA VPS34-CII bound to RAB5A-GTP 1-212 (C19S, C63S, Q79L) on the VPS15 subunit Deposited 2025-07-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–450（450 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 4.00 Å
9RXB VPS34-CII (VPS34/VPS15/BECLIN1/UVRAG) bound to RAB5A (Q79L) on the VPS34 and VPS15 subunits Deposited 2025-07-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–450（450 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 4.03 Å
9S47 Human complex II-BATS bound to membrane-attached Rab5a-GTP Deposited 2025-07-25 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–450（450 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 9.88 Å
9ZPC Cryo-EM structure of human PI3KC3-C2 Deposited 2025-12-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–450（450 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.83 Å
9ZPD Cryo-EM structure of human PI3KC3-C2 in complex with Rubicon Middle Region of C terminus Deposited 2025-12-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–450（450 aa）
Chain E 1–450（450 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å

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

View Construct and Data Evidence
UniProt name BECN1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain E； PDBConstruct 1–26； UniProt 105–130 Author chain F； PDBConstruct 1–26； UniProt 105–130 Author chain G； PDBConstruct 1–26； UniProt 105–130 Author chain H； PDBConstruct 1–26； UniProt 105–130

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 5vau

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5vau
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5vau
Deposition date deposition_date2017-03-28
Structure title titleBcl-2 complex with Beclin 1 BH3 domain
Keywords keywordsapoptosis, Bcl-2, autophagy, Beclin 1; 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_guinier34.93 Å
Radius of gyration Rg (electron density) rg_electron34.64 Å
Forward intensity I(0) i087662400.00
Molecular weight molecular_weight73932.0 kDa
Excluded volume excluded_volume91890 ų
Envelope volume envelope_volume121270 ų
Hydration-shell volume shell_volume30504 ų
Envelope diameter envelope_diameter116.7 Å
Shell Rg shell_rg39.32 Å
Envelope Rg envelope_rg34.03 Å
Shape Rg shape_rg34.65 Å
Total Rg total_rg34.95 Å
Total atoms total_atoms5219
Residues n_residues644
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 dmax117.9 Å
Rg (real space) rg_real35.10 Å
Rg uncertainty (real space) rg_real_error1.05 Å
I(0) (real space) i0_real8.7660e+07
I(0) uncertainty (real space) i0_real_error1.4860e+06
Rg (reciprocal space) rg_reciprocal35.00 Å
I(0) (reciprocal space) i0_reciprocal87650000.0000
Solution quality estimate total_estimate0.5867
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.2 Å
Skewness Skewness skewness0.352
Kurtosis Kurtosis kurtosis-0.619
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha61220000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.775; Stabil: 1.000; Sysdev: 0.186; Positv: 1.000; Valcen: 0.739; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)