SMTL ID : 2nl9.3 (2 other biounits)

Crystal structure of the Mcl-1:Bim BH3 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-4-4-mer

Ligands

28 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: E.122 Chain C: E.70, D.71 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:D.71, C:D.71, A:E.122, A:E.122, H2O.17 ZN.2: 3 residues within 4Å: Chain A: D.143, E.147 Chain H: E.18 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain H Metal complexes: A:D.143, A:D.143, A:E.147, H:E.18, H:E.18 ZN.3: 3 residues within 4Å: Chain A: H.82 Chain B: D.134 Ligands: ZN.4 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.134, B:D.134, A:H.82, H2O.5 ZN.4: 3 residues within 4Å: Chain A: H.82 Chain B: D.134 Ligands: ZN.3 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.134, B:D.134, A:H.82, H2O.5, H2O.5 ZN.5: 4 residues within 4Å: Chain A: C.116, I.117 Ligands: ZN.6, ZN.20 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:C.116, H2O.4, H2O.4, H2O.4 ZN.6: 6 residues within 4Å: Chain A: C.116 Chain C: C.116, E.118 Ligands: ZN.5, ZN.19, ZN.20 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:C.116, A:C.116, H2O.5, H2O.17 ZN.8: 3 residues within 4Å: Chain B: E.122 Chain D: E.70, D.71 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:E.122, B:E.122, D:D.71, D:D.71, H2O.23 ZN.9: 3 residues within 4Å: Chain B: D.143, E.147 Chain G: E.18 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain G Metal complexes: B:D.143, B:D.143, B:E.147, G:E.18, G:E.18 ZN.10: 3 residues within 4Å: Chain A: D.134 Chain B: H.82 Ligands: ZN.11 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.134, A:D.134, B:H.82, H2O.11 ZN.11: 3 residues within 4Å: Chain A: D.134 Chain B: H.82 Ligands: ZN.10 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.134, A:D.134, B:H.82, H2O.11, H2O.11 ZN.12: 4 residues within 4Å: Chain B: C.116, I.117 Ligands: ZN.13, ZN.27 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:C.116, H2O.11, H2O.11, H2O.11 ZN.13: 6 residues within 4Å: Chain B: C.116 Chain D: C.116, E.118 Ligands: ZN.12, ZN.26, ZN.27 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:C.116, D:C.116, H2O.11, H2O.24 ZN.15: 3 residues within 4Å: Chain A: E.70, D.71 Chain C: E.122 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:E.122, C:E.122, A:D.71, A:D.71, H2O.4 ZN.16: 3 residues within 4Å: Chain C: D.143, E.147 Chain F: E.18 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain F Metal complexes: C:D.143, C:D.143, C:E.147, F:E.18, F:E.18 ZN.17: 3 residues within 4Å: Chain C: H.82 Chain D: D.134 Ligands: ZN.18 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:D.134, D:D.134, C:H.82, H2O.17 ZN.18: 3 residues within 4Å: Chain C: H.82 Chain D: D.134 Ligands: ZN.17 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:D.134, D:D.134, C:H.82, H2O.17, H2O.17 ZN.19: 4 residues within 4Å: Chain C: C.116, I.117 Ligands: ZN.6, ZN.20 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:C.116, H2O.17, H2O.17, H2O.17 ZN.20: 6 residues within 4Å: Chain A: C.116, E.118 Chain C: C.116 Ligands: ZN.5, ZN.6, ZN.19 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: A:C.116, C:C.116, H2O.5, H2O.17 ZN.22: 3 residues within 4Å: Chain B: E.70, D.71 Chain D: E.122 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:D.71, B:D.71, D:E.122, D:E.122, H2O.10 ZN.23: 3 residues within 4Å: Chain D: D.143, E.147 Chain E: E.18 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain D Metal complexes: E:E.18, E:E.18, D:D.143, D:D.143, D:E.147 ZN.24: 3 residues within 4Å: Chain C: D.134 Chain D: H.82 Ligands: ZN.25 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:D.134, C:D.134, D:H.82, H2O.23 ZN.25: 3 residues within 4Å: Chain C: D.134 Chain D: H.82 Ligands: ZN.24 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:D.134, C:D.134, D:H.82, H2O.23, H2O.23 ZN.26: 4 residues within 4Å: Chain D: C.116, I.117 Ligands: ZN.13, ZN.27 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:C.116, H2O.23, H2O.23, H2O.23 ZN.27: 6 residues within 4Å: Chain B: C.116, E.118 Chain D: C.116 Ligands: ZN.12, ZN.13, ZN.26 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:C.116, D:C.116, H2O.11, H2O.24 ZN.29: 3 residues within 4Å: Chain D: H.150, E.152 Chain E: E.11 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: D:H.150, D:E.152, E:E.11, E:E.11, H2O.26 ZN.30: 3 residues within 4Å: Chain C: H.150, E.152 Chain F: E.11 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: C:H.150, C:E.152, F:E.11, F:E.11, H2O.28 ZN.31: 3 residues within 4Å: Chain B: H.150, E.152 Chain G: E.11 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: B:H.150, B:E.152, G:E.11, G:E.11, H2O.29 ZN.32: 3 residues within 4Å: Chain A: H.150, E.152 Chain H: E.11 5 PLIP interactions: 2 interactions with chain H, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: H:E.11, H:E.11, A:H.150, A:E.152, H2O.31

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 5 residues within 4Å: Chain A: I.81, R.130 Chain B: I.81, R.130 Ligands: CL.14 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain A: I.81, R.130 Chain B: I.81, R.130 Ligands: CL.7 Ligand excluded by PLIP CL.21: 5 residues within 4Å: Chain C: I.81, R.130 Chain D: I.81, R.130 Ligands: CL.28 Ligand excluded by PLIP CL.28: 5 residues within 4Å: Chain C: I.81, R.130 Chain D: I.81, R.130 Ligands: CL.21 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Czabotar, P.E. et al., Structural insights into the degradation of Mcl-1 induced by BH3 domains. Proc.Natl.Acad.Sci.USA (2007)

Release Date

2007-03-27

Peptides

FUSION PROTEIN CONSISTING OF Induced myeloid leukemia cell differentiation protein Mcl-1 homolog: ABCD
Bcl-2-like protein 11: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
B

F
B

G
B

H
B

FUSION PROTEIN CONSISTING OF Induced myeloid leukemia cell differentiation protein Mcl-1 homolog

Bcl-2-like protein 11

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