8t5e

De novo design of high-affinity protein binders to bioactive helical peptides

Method: X-RAY DIFFRACTION D_max: 51.2 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Bcl-2-like protein 11

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 141–166	Not recorded	Bim_fulldiff × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；0.1 M Citric acid pH 2.5, 20% (w/v) PEG 6000	Resolution 3.00 Å R-free 0.264

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 8T5E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1F95 SOLUTION STRUCTURE OF DYNEIN LIGHT CHAIN 8 (DLC8) AND BIM PEPTIDE COMPLEX Deposited 2000-07-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 108–116（9 aa） Fragment：DLC8 BINDING REGION Chain D 108–116（9 aa） Fragment：DLC8 BINDING REGION	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 100mM；Pressure ambient NMR sample composition 1.5mM DLC8/Bim peptide complex 15N; 100mM phosphate buffer; 10mM DTT; 90% H2O and 10% D2O \| 90% H2O and 10% D2O NMR sample composition 1.5mM DLC8/Bim peptide complex 15N,13C; 100mM phosphate buffer; 10mM DTT; 90% H2O and 10% D2O \| 90% H2O and 10% D2O NMR sample composition 1.5mM DLC8/Bim peptide complex ; 100mM phosphate buffer; 10mM DTT; 99.9% D2O \| 99.9% D2O	Resolution not provided
2K7W BAX Activation is Initiated at a Novel Interaction Site Deposited 2008-08-27	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 145–164（20 aa） Fragment：BIM BH3 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；305 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition 0.1-0.2 mM [U-99% 15N] protein, 0.1-0.2 mM peptide, 90% H2O/10%D20 \| 90% H2O/10%D20	Resolution not provided
2NL9 Crystal structure of the Mcl-1:Bim BH3 complex Deposited 2006-10-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 141–166（26 aa）	Not recorded	ZN ZINC ION × 7 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.75；298 K；0.2M zinc acetate, 0.2M imidazole, 2mM TCEP, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.55 Å R-free 0.203
2NL9 Crystal structure of the Mcl-1:Bim BH3 complex Deposited 2006-10-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain B 141–166（26 aa）	Not recorded	ZN ZINC ION × 28 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.75；298 K；0.2M zinc acetate, 0.2M imidazole, 2mM TCEP, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.55 Å R-free 0.203
2NL9 Crystal structure of the Mcl-1:Bim BH3 complex Deposited 2006-10-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain B 141–166（26 aa）	Not recorded	ZN ZINC ION × 28 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.75；298 K；0.2M zinc acetate, 0.2M imidazole, 2mM TCEP, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.55 Å R-free 0.203
2V6Q Crystal Structure of a BHRF-1 : Bim BH3 complex Deposited 2007-07-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 141–166（26 aa） Fragment：RESIDUES 141-166	Not recorded	BR BROMIDE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 4；0.1 M MALIC ACID PH 4.0, 1.7 M NABR, 0.1 M GUANIDINE HCL	Resolution 2.70 Å R-free 0.249
2VM6 Human Bcl2-A1 in complex with Bim-BH3 peptide Deposited 2008-01-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 141–165（25 aa） Fragment：RESIDUES 141-165	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；0.1M BIS, TRIS PH 5.8, 2M AMSO4	Resolution 2.20 Å R-free 0.250
2WH6 Crystal structure of anti-apoptotic BHRF1 in complex with the Bim BH3 domain Deposited 2009-05-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 51–76（26 aa） Fragment：BH3, RESIDUES 51-72	Not recorded	BR BROMIDE ION × 9 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4；0.1 M MALIC ACID PH 4 1.25 M NABR	Resolution 1.50 Å R-free 0.205
2YQ6 Structure of Bcl-xL bound to BimSAHB Deposited 2012-11-06	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 B 147–164（18 aa） Fragment：BH3 DOMAIN, RESIDUES 14-31	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 14	X-RAY DIFFRACTION X-ray crystallization conditions 15 % (W/V) PEG 400, 5 % PEG 3000, 10 % GLYCEROL AND 0.1 M MES PH 6.5.	Resolution 1.80 Å R-free 0.201
2YQ7 Structure of Bcl-xL bound to BimLOCK Deposited 2012-11-06	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 B 147–164（18 aa） Fragment：BH3 DOMAIN, RESIDUES 147-164	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions 15 % (W/V) PEG 400, 5 % PEG 3000, 10 % GLYCEROL AND 0.1 M MES PH 6.5.	Resolution 1.90 Å R-free 0.208
3D7V Crystal structure of Mcl-1 in complex with an Mcl-1 selective BH3 ligand Deposited 2008-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 141–166（26 aa） Fragment：Bim BH3	Mutation：L62A, F69A	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.75；298 K；0.2M Zinc Acetate, 0.2M Imidazole, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.03 Å R-free 0.241
3FDL Bim BH3 peptide in complex with Bcl-xL Deposited 2008-11-26	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 141–166（26 aa） Fragment：BH3 domain, UNP residues 141-166	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；1M Sodium citrate, 0.1M Sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.78 Å R-free 0.208
3FDL Bim BH3 peptide in complex with Bcl-xL Deposited 2008-11-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 141–166（26 aa） Fragment：BH3 domain, UNP residues 141-166	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；1M Sodium citrate, 0.1M Sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.78 Å R-free 0.208
3IO8 BimL12F in complex with Bcl-xL Deposited 2009-08-14	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 141–166（26 aa） Fragment：BH3 peptide, residues 141-166	Mutation：L152P	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.02M Zinc Acetate 2.5M Sodium Chloride 0.1M Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.231
3IO8 BimL12F in complex with Bcl-xL Deposited 2009-08-14	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 141–166（26 aa） Fragment：BH3 peptide, residues 141-166	Mutation：L152P	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.02M Zinc Acetate 2.5M Sodium Chloride 0.1M Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.231
3IO9 BimL12Y in complex with Mcl-1 Deposited 2009-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 141–166（26 aa） Fragment：BH3 peptide, residues 141-166	Mutation：L152P	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.75；298 K；0.15M zinc acetate, 0.15 M imidizole, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.251
3KJ0 Mcl-1 in complex with Bim BH3 mutant I2dY Deposited 2009-11-02	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 143–165（23 aa） Fragment：BH3 region of BIM (UNP 1-23)	Mutation：I6Y	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M Tris, 45% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.224
3KJ1 Mcl-1 in complex with Bim BH3 mutant I2dA Deposited 2009-11-02	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 143–163（21 aa） Fragment：BH3 region of BIM (UNP 1-21)	Mutation：I6A	ZN ZINC ION × 5 ACT ACETATE ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1 M Imidazole, 0.2 M Zinc Acetate, 16% PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.95 Å R-free 0.213
3KJ1 Mcl-1 in complex with Bim BH3 mutant I2dA Deposited 2009-11-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 143–163（21 aa） Fragment：BH3 region of BIM (UNP 1-21)	Mutation：I6A	ZN ZINC ION × 20 ACT ACETATE ION × 4 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1 M Imidazole, 0.2 M Zinc Acetate, 16% PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.95 Å R-free 0.213
3KJ2 Mcl-1 in complex with Bim BH3 mutant F4aE Deposited 2009-11-02	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 143–163（21 aa） Fragment：BH3 region of Bim (UNP 1-21)	Mutation：F17E	ZN ZINC ION × 4 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1 M Imidazole, 0.2 M Zinc Acetate, 2% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.35 Å R-free 0.247
3KJ2 Mcl-1 in complex with Bim BH3 mutant F4aE Deposited 2009-11-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 143–163（21 aa） Fragment：BH3 region of Bim (UNP 1-21)	Mutation：F17E	ZN ZINC ION × 16 ACT ACETATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1 M Imidazole, 0.2 M Zinc Acetate, 2% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.35 Å R-free 0.247
4B4S Crystal Structure of a pro-survival Bcl-2:Bim BH3 complex Deposited 2012-08-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 51–76（26 aa） Fragment：RESIDUES 51-76	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；0.1 M MGCL2, 20 % PEG 400, 20 % PEG 3350, 0.1 M TRIS PH 8.0	Resolution 1.90 Å R-free 0.220
4D2M Vaccinia Virus F1L bound to Bim BH3 Deposited 2014-05-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 141–166（26 aa） Fragment：RESIDUES 141-166 Chain D 141–166（26 aa） Fragment：RESIDUES 141-166	Not recorded	MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 2 CL CHLORIDE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；0.2M KCL, 15 % PEG400, 1.44 % MPD AND 0.1M AMMONIUM CITRATE PH 6.2.	Resolution 2.10 Å R-free 0.255
4QVF Crystal structure of Bcl-xL in complex with BIM BH3 domain Deposited 2014-07-15	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 141–166（26 aa） Fragment：UNP residues 141-166	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；291 K；17.5% PEG 8000, 0.2M NaCl, 0.1M phosphate citrate pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.53 Å R-free 0.230
4UF3 Deerpox virus DPV022 in complex with Bim BH3 Deposited 2014-12-23	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 141–166（26 aa） Fragment：BH3, UNP RESIDUES 141-166	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；17% PEG 8000, 0.2M MES PH 5.5, 0.2M AMMONIUM SULPHATE	Resolution 2.70 Å R-free 0.221
4ZIE Crystal Structure of core/latch dimer of Bax in complex with BimBH3 Deposited 2015-04-28	Different construct 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 141–166（26 aa） Fragment：BH3 motif, UNP RESIDUES 141-166	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；277 K；PEG6000, bicine	Resolution 1.80 Å R-free 0.229
4ZIF Crystal Structure of core/latch dimer of Bax in complex with BimBH3mini Deposited 2015-04-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 141–160（20 aa） Fragment：BH3 motif, unp residues 141-160	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；Tri-sodium citrate, Sodium cacodylate	Resolution 2.40 Å R-free 0.255
4ZIH Crystal Structure of core/latch dimer of Bax in complex with BimBH3mini Deposited 2015-04-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 141–160（20 aa） Fragment：BH3 motif, unp residues 141-160	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；Tri-sodium citrate, Sodium cacodylate	Resolution 2.50 Å R-free 0.233
5AGW Bcl-2 alpha beta-1 complex Deposited 2015-02-04	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 C 146–166（21 aa） Fragment：RESIDUES 148-166	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 146–166（21 aa） Fragment：RESIDUES 148-166	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 146–166（21 aa） Fragment：BIM BH3, RESIDUES 146-166	Non-standard monomer：Yes (specific site not provided by mmCIF)	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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 146–166（21 aa） Fragment：BIM BH3, RESIDUES 146-166	Non-standard monomer：Yes (specific site not provided by mmCIF)	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
5C3G Crystal structure of Bcl-xl bound to BIM-MM Deposited 2015-06-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 56–76（21 aa） Fragment：UNP residues 56-76	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；12% Peg 1500, 0.1M Sodium Acetate pH 5.5, 2.5M NaCl, 1.5% MPD	Resolution 2.45 Å R-free 0.274
5VWV Bak core latch dimer in complex with Bim-BH3 - Cubic Deposited 2017-05-23	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 141–165（25 aa） Fragment：UNP residues 141-165	Mutation：W147R, Y163T	TFA trifluoroacetic acid × 1 EDO 1,2-ETHANEDIOL × 6 CL CHLORIDE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；18 % glycerol, 21.6 % PEG (poly-ethylene glycol) 1500 and 0.5 % ethyl acetate	Resolution 1.90 Å R-free 0.177
5VWV Bak core latch dimer in complex with Bim-BH3 - Cubic Deposited 2017-05-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 141–165（25 aa） Fragment：UNP residues 141-165	Mutation：W147R, Y163T	TFA trifluoroacetic acid × 2 EDO 1,2-ETHANEDIOL × 12 CL CHLORIDE ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；18 % glycerol, 21.6 % PEG (poly-ethylene glycol) 1500 and 0.5 % ethyl acetate	Resolution 1.90 Å R-free 0.177
5VWW Bak core latch dimer in complex with Bim-RT - Tetragonal Deposited 2017-05-23	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 141–166（26 aa） Fragment：UNP residues 141-166 Chain D 141–166（26 aa） Fragment：UNP residues 141-166	Mutation：W147R, Y163T Mutation：W147R, Y163T	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 BR BROMIDE ION × 2 IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；281 K；12.5 % MPD (2-methyl-2,4-pentanediol), 38 mM imidazole pH 6.5, 12.5 % PEG 1000, 12.5 % PEG 3350, 30 mM sodium fluoride, 30 mM sodium iodide, 62 mM sodium MES pH 6.5 and 30 mM sodium bromide	Resolution 2.80 Å R-free 0.281
5VWX Bak core latch dimer in complex with Bim-h0-h3Glt Deposited 2017-05-23	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 B 142–164（23 aa） Fragment：UNP residues 142-164 Chain D 142–164（23 aa） Fragment：UNP residues 142-164	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；281 K；200 mM calcium acetate, 30 % PEG 400 and 100 mM sodium acetate-acetic acid pH 5.0	Resolution 2.49 Å R-free 0.305
5VWY Bak core latch dimer in complex with Bim-h3Pc-RT Deposited 2017-05-23	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 B 141–166（26 aa） Fragment：UNP residues 141-166	Mutation：W147R, Y163T Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；277 K；15.8 % PEG 8000, 50 mM potassium dihydrogen phosphate, and 22.7 % glycerol	Resolution 1.55 Å R-free 0.216
5VWZ Bak in complex with Bim-h3Pc Deposited 2017-05-23	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 B 141–166（26 aa） Fragment：UNP residues 141-166 Chain D 141–166（26 aa） Fragment：UNP residues 141-166	Mutation：W147R, Y163T Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：W147R, Y163T Non-standard monomer：Yes (specific site not provided by mmCIF)	1PG 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL × 2 NH4 AMMONIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；281 K；10 % PEG 20000, 20 % PEG MME 550, 38 mM Imidazole pH 6.5, 20 mM ammonium acetate, 20 mM potassium sodium tartrate, 20 mM sodium formate, 62 mM sodium MES pH 6.5, 20 mM trisodium citrate, and 20 mM sodium oxamate	Resolution 1.62 Å R-free 0.191
5VX0 Bak in complex with Bim-h3Glg Deposited 2017-05-23	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 B 141–166（26 aa） Fragment：UNP residues 141-166 Chain D 141–166（26 aa） Fragment：UNP residues 141-166	Mutation：W147R, Y163T Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：W147R, Y163T Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 6 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；281 K；200 mM magnesium chloride, 25 % PEG 3350, and 100 mM bis-tris chloride (pH 6.5)	Resolution 1.60 Å R-free 0.200
5VX2 Mcl-1 in complex with Bim-h3Pc-RT Deposited 2017-05-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 141–166（26 aa） Fragment：UNP residues 141-166 Chain D 141–166（26 aa） Fragment：UNP residues 141-166	Mutation：W147R, Y163T Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：W147R, Y163T Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；281 K；20 % PEG 3000, 100 mM trisodium citrate buffered with citric acid pH 5.5	Resolution 1.85 Å R-free 0.210
5VX3 Bcl-xL in complex with Bim-h3Pc-RT Deposited 2017-05-23	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 B 141–166（26 aa） Fragment：UNP residues 141-166 Chain F 141–166（26 aa） Fragment：UNP residues 141-166	Mutation：W147R, Y163T Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：W147R, Y163T Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；273 K；200 mM magnesium chloride, 20 % PEG 6000, and 100 mM sodium MES pH 6	Resolution 1.95 Å R-free 0.243
5VX3 Bcl-xL in complex with Bim-h3Pc-RT Deposited 2017-05-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 141–166（26 aa） Fragment：UNP residues 141-166 Chain H 141–166（26 aa） Fragment：UNP residues 141-166	Mutation：W147R, Y163T Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：W147R, Y163T Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；273 K；200 mM magnesium chloride, 20 % PEG 6000, and 100 mM sodium MES pH 6	Resolution 1.95 Å R-free 0.243
5WOS Structural and functional insights into Canarypox Virus CNP058 regulation of apoptosis Deposited 2017-08-02	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 141–166（26 aa） Fragment：BH3 domain (UNP residues 141-166)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；0.2 M calcium chloride dihydrate, 0.1 M MES pH 6.0, 20% w/v PEG6000	Resolution 2.45 Å R-free 0.245
6QFI Structure of human Mcl-1 in complex with BIM BH3 peptide Deposited 2019-01-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 141–166（26 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.75；293 K；0.2M zinc acetate, 0.2M Imidazole pH 5.75	Resolution 2.40 Å R-free 0.236
6RJP Bfl-1 in complex with alpha helical peptide Deposited 2019-04-29	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 147–163（17 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.1 M sodium acetate pH 4.6 16% (w/v) PEG smear high	Resolution 2.57 Å R-free 0.266
6RJP Bfl-1 in complex with alpha helical peptide Deposited 2019-04-29	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 147–163（17 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.1 M sodium acetate pH 4.6 16% (w/v) PEG smear high	Resolution 2.57 Å R-free 0.266
6TQQ Structural insight into tanapoxvirus mediated inhibition of apoptosis Deposited 2019-12-17	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 141–166（26 aa）	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M MIB pH 8.0, 25% PEG 1500	Resolution 3.00 Å R-free 0.276
6X8O BimBH3 peptide tetramer Deposited 2020-06-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 141–166（26 aa） Chain B 141–166（26 aa） Chain C 141–166（26 aa） Chain D 141–166（26 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SCN THIOCYANATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG600, 0.05 M Tris-HCl, 0.15 M potassium thiocyanate, 0.5% CHAPS	Resolution 1.31 Å R-free 0.168

38 other PDB entries and 49 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	B2L11_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–26； UniProt 141–166

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8t5e
Deposition date deposition_date	2023-06-13
Structure title title	De novo design of high-affinity protein binders to bioactive helical peptides
Keywords keywords	Alpha-helical peptides, protein design, diffusion, deep learning, DE NOVO PROTEIN; DE NOVO PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	16.43 Å
Radius of gyration Rg (electron density) rg_electron	14.98 Å
Forward intensity I(0) i0	6265480.00
Molecular weight molecular_weight	17753.0 kDa
Excluded volume excluded_volume	22174 Å³
Envelope volume envelope_volume	25412 Å³
Hydration-shell volume shell_volume	14138 Å³
Envelope diameter envelope_diameter	50.8 Å
Shell Rg shell_rg	21.19 Å
Envelope Rg envelope_rg	15.42 Å
Shape Rg shape_rg	15.00 Å
Total Rg total_rg	16.09 Å
Total atoms total_atoms	1244
Residues n_residues	152
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	51.2 Å
Rg (real space) rg_real	16.32 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	6.2650e+06
I(0) uncertainty (real space) i0_real_error	7.6470e+04
Rg (reciprocal space) rg_reciprocal	16.33 Å
I(0) (reciprocal space) i0_reciprocal	6266000.0000
Solution quality estimate total_estimate	0.8172
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.3 Å
Skewness Skewness skewness	0.165
Kurtosis Kurtosis kurtosis	-0.379
Angular range angular_range	— – 0.4850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1611000.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	25.790 Å
Unit-cell length b length_b	66.667 Å
Unit-cell length c length_c	74.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	49.620 Å
R factor r_factor	0.2408
R_work r_work	0.2392
R_free r_free	0.2644

Description description	Bim_fulldiff
Molecular weight formula_weight	16226.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1244

De novo design of high-affinity protein binders to bioactive helical peptides

1. Protein Identity and Related Structures Protein Identity & Related Structures

Bcl-2-like protein 11

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	synthetic construct
NCBI Class编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/t5/8t5e/8t5e.fit
pddf	/app/data/pr_computation/t5/8t5e/8t5e.pr.out
profile	/app/data/saxs_computation/t5/8t5e/8t5e.dat