SMTL ID : 2pqk.3 (5 other biounits)

X-ray crystal structure of human Mcl-1 in complex with Bim BH3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-4-4-mer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 2 residues within 4Å: Chain A: D.135 Chain B: H.83 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:H.83, A:D.135, A:D.135, H2O.2, H2O.3 ZN.2: 3 residues within 4Å: Chain A: D.144, E.148 Chain H: E.20 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain H Metal complexes: A:D.144, A:D.144, A:E.148, H:E.20, H:E.20 ZN.4: 2 residues within 4Å: Chain A: H.83 Chain B: D.135 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.83, B:D.135, B:D.135, H2O.6, H2O.7 ZN.5: 3 residues within 4Å: Chain B: D.144, E.148 Chain G: E.20 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain G Metal complexes: B:D.144, B:D.144, B:E.148, G:E.20, G:E.20 ZN.7: 2 residues within 4Å: Chain C: D.135 Chain D: H.83 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:H.83, C:D.135, C:D.135, H2O.9, H2O.11 ZN.8: 3 residues within 4Å: Chain C: D.144, E.148 Chain F: E.20 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain C Metal complexes: F:E.20, F:E.20, C:D.144, C:D.144, C:E.148 ZN.10: 2 residues within 4Å: Chain C: H.83 Chain D: D.135 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:D.135, D:D.135, C:H.83, H2O.13, H2O.14 ZN.11: 3 residues within 4Å: Chain D: D.144, E.148 Chain E: E.20 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain D Metal complexes: E:E.20, E:E.20, D:D.144, D:D.144, D:E.148 ZN.13: 2 residues within 4Å: Chain D: H.151 Chain E: E.13 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: E:E.13, E:E.13, D:H.151, H2O.16, H2O.16 ZN.14: 2 residues within 4Å: Chain C: H.151 Chain F: E.13 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: C:H.151, F:E.13, F:E.13, H2O.16, H2O.17 ZN.15: 2 residues within 4Å: Chain B: H.151 Chain G: E.13 5 PLIP interactions: 2 interactions with chain G, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: G:E.13, G:E.13, B:H.151, H2O.17, H2O.18 ZN.16: 2 residues within 4Å: Chain A: H.151 Chain H: E.13 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: A:H.151, H:E.13, H:E.13, H2O.18, H2O.18

4 x NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Chain A: E.71, D.72 Chain C: E.123 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.123 NA.6: 3 residues within 4Å: Chain B: E.71, D.72 Chain D: E.123 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.72 NA.9: 3 residues within 4Å: Chain A: E.123 Chain C: E.71, D.72 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.71, C:E.71 NA.12: 3 residues within 4Å: Chain B: E.123 Chain D: E.71, D.72 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.71, D:E.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fire, E. et al., Mcl-1-Bim complexes accommodate surprising point mutations via minor structural changes. Protein Sci. (2010)

Release Date

2007-06-19

Peptides

Induced myeloid leukemia cell differentiation protein Mcl-1: ABCD
Bim BH3 peptide: 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

Induced myeloid leukemia cell differentiation protein Mcl-1

Bim BH3 peptide

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