SMTL ID : 3kj1.2 (1 other biounit)

Mcl-1 in complex with Bim BH3 mutant I2dA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-4-4-mer

Ligands

20 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.83 Chain C: D.135 Ligands: ACT.5 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:D.135, C:D.135, A:H.83, H2O.9 ZN.2: 3 residues within 4Å: Chain A: E.123 Chain E: E.71, D.72 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain A Metal complexes: E:E.71, E:D.72, E:D.72, A:E.123, A:E.123 ZN.3: 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: 2 residues within 4Å: Chain A: Q.60, H.108 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.108 ZN.7: 2 residues within 4Å: Chain B: W.5, E.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.9, B:E.9, H2O.4 ZN.8: 3 residues within 4Å: Chain A: D.135 Chain C: H.83 Ligands: ACT.12 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:D.135, A:D.135, C:H.83, H2O.4 ZN.9: 3 residues within 4Å: Chain C: E.123 Chain G: E.71, D.72 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain C Metal complexes: G:E.71, G:D.72, G:D.72, C:E.123, C:E.123 ZN.10: 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.11: 2 residues within 4Å: Chain C: Q.60, H.108 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.108 ZN.14: 2 residues within 4Å: Chain D: W.5, E.9 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.9, D:E.9, H2O.9 ZN.15: 3 residues within 4Å: Chain E: H.83 Chain G: D.135 Ligands: ACT.19 4 PLIP interactions: 2 interactions with chain G, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: G:D.135, G:D.135, E:H.83, H2O.18 ZN.16: 3 residues within 4Å: Chain A: E.71, D.72 Chain E: E.123 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain E Metal complexes: A:E.71, A:D.72, A:D.72, E:E.123, E:E.123 ZN.17: 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.18: 2 residues within 4Å: Chain E: Q.60, H.108 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.108 ZN.21: 2 residues within 4Å: Chain F: W.5, E.9 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.9, F:E.9, H2O.13 ZN.22: 3 residues within 4Å: Chain E: D.135 Chain G: H.83 Ligands: ACT.26 4 PLIP interactions: 1 interactions with chain G, 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: G:H.83, E:D.135, E:D.135, H2O.13 ZN.23: 3 residues within 4Å: Chain C: E.71, D.72 Chain G: E.123 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain G Metal complexes: C:E.71, C:D.72, C:D.72, G:E.123, G:E.123 ZN.24: 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.25: 2 residues within 4Å: Chain G: Q.60, H.108 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:H.108 ZN.28: 2 residues within 4Å: Chain H: W.5, E.9 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.9, H:E.9, H2O.18

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 6 residues within 4Å: Chain A: H.83 Chain B: A.7, Q.8, R.11 Chain C: D.135 Ligands: ZN.1 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Q.8 Water bridges: B:R.11, B:R.11 Salt bridges: B:R.11, A:H.83 ACT.12: 6 residues within 4Å: Chain A: D.135 Chain C: H.83 Chain D: A.7, Q.8, R.11 Ligands: ZN.8 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Q.8 Water bridges: D:R.11, D:R.11 Salt bridges: D:R.11, C:H.83 ACT.19: 6 residues within 4Å: Chain E: H.83 Chain F: A.7, Q.8, R.11 Chain G: D.135 Ligands: ZN.15 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:Q.8 Water bridges: F:R.11, F:R.11 Salt bridges: F:R.11, E:H.83 ACT.26: 6 residues within 4Å: Chain E: D.135 Chain G: H.83 Chain H: A.7, Q.8, R.11 Ligands: ZN.22 6 PLIP interactions: 2 interactions with chain G, 4 interactions with chain H Water bridges: G:H.83, H:R.11, H:R.11 Salt bridges: G:H.83, H:R.11 Hydrophobic interactions: H:Q.8

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

CL.6: 5 residues within 4Å: Chain A: I.82, R.131 Chain C: I.82, R.131 Ligands: CL.13 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain A: I.82, R.131 Chain C: I.82, R.131 Ligands: CL.6 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain E: I.82, R.131 Chain G: I.82, R.131 Ligands: CL.27 Ligand excluded by PLIP CL.27: 5 residues within 4Å: Chain E: I.82, R.131 Chain G: I.82, R.131 Ligands: CL.20 Ligand excluded by PLIP

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

2010-02-16

Peptides

Induced myeloid leukemia cell differentiation protein Mcl-1: ACEG
Bcl-2-like protein 11: 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

Bcl-2-like protein 11

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