SMTL ID : 2pqk.2 (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 C: H.83 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: A:D.135, A:D.135, C:H.83, H2O.2, H2O.3 ZN.2: 2 residues within 4Å: Chain A: D.144, E.148 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.144, A:D.144, A:E.148 ZN.4: 1 residues within 4Å: Chain B: E.13 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.13, B:E.13, H2O.5, H2O.5 ZN.5: 2 residues within 4Å: Chain A: H.83 Chain C: D.135 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: A:H.83, C:D.135, C:D.135, H2O.7, H2O.8 ZN.6: 2 residues within 4Å: Chain C: D.144, E.148 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.144, C:D.144, C:E.148 ZN.8: 1 residues within 4Å: Chain D: E.13 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.13, D:E.13, H2O.9, H2O.9 ZN.9: 2 residues within 4Å: Chain E: D.135 Chain G: H.83 5 PLIP interactions: 1 interactions with chain G, 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: G:H.83, E:D.135, E:D.135, H2O.11, H2O.12 ZN.10: 2 residues within 4Å: Chain E: D.144, E.148 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.144, E:D.144, E:E.148 ZN.12: 1 residues within 4Å: Chain F: E.13 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.13, F:E.13, H2O.14, H2O.14 ZN.13: 2 residues within 4Å: Chain E: H.83 Chain G: D.135 5 PLIP interactions: 2 interactions with chain G, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: G:D.135, G:D.135, E:H.83, H2O.16, H2O.17 ZN.14: 2 residues within 4Å: Chain G: D.144, E.148 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:D.144, G:D.144, G:E.148 ZN.16: 1 residues within 4Å: Chain H: E.13 4 PLIP interactions: 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: 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 E: E.123 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.123 NA.7: 3 residues within 4Å: Chain C: E.71, D.72 Chain G: E.123 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.71 NA.11: 3 residues within 4Å: Chain A: E.123 Chain E: E.71, D.72 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.71, E:E.71 NA.15: 3 residues within 4Å: Chain C: E.123 Chain G: E.71, D.72 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain C Hydrogen bonds: G:E.71, C:E.123

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: ACEG
Bim BH3 peptide: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

B
B

D
B

F
B

H
B

Induced myeloid leukemia cell differentiation protein Mcl-1

Bim BH3 peptide

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