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

Crystal structure of the Mcl-1:Bim BH3 complex

Coordinates

PDB Format

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 E: E.70, D.71 5 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: E:D.71, E:D.71, A:E.122, A:E.122, H2O.20 ZN.2: 2 residues within 4Å: Chain A: D.143, E.147 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.143, A:D.143, A:E.147 ZN.3: 4 residues within 4Å: Chain A: H.82 Chain B: R.13 Chain C: D.134 Ligands: ZN.4 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:D.134, C:D.134, A:H.82, H2O.5, H2O.8 ZN.4: 3 residues within 4Å: Chain A: H.82 Chain C: D.134 Ligands: ZN.3 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:D.134, C: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.22 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 E: C.116, E.118 Ligands: ZN.5, ZN.21, ZN.22 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: A:C.116, E:C.116, H2O.5, H2O.20 ZN.8: 1 residues within 4Å: Chain B: E.11 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.11, B:E.11, H2O.8 ZN.9: 3 residues within 4Å: Chain C: E.122 Chain G: E.70, D.71 5 PLIP interactions: 2 interactions with chain G, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: G:D.71, G:D.71, C:E.122, C:E.122, H2O.27 ZN.10: 2 residues within 4Å: Chain C: D.143, E.147 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.143, C:D.143, C:E.147 ZN.11: 4 residues within 4Å: Chain A: D.134 Chain C: H.82 Chain D: R.13 Ligands: ZN.12 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: A:D.134, A:D.134, C:H.82, H2O.12, H2O.16 ZN.12: 3 residues within 4Å: Chain A: D.134 Chain C: H.82 Ligands: ZN.11 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: A:D.134, A:D.134, C:H.82, H2O.12, H2O.12 ZN.13: 4 residues within 4Å: Chain C: C.116, I.117 Ligands: ZN.14, ZN.30 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:C.116, H2O.12, H2O.12, H2O.12 ZN.14: 6 residues within 4Å: Chain C: C.116 Chain G: C.116, E.118 Ligands: ZN.13, ZN.29, ZN.30 4 PLIP interactions: 1 interactions with chain G, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: G:C.116, C:C.116, H2O.13, H2O.28 ZN.16: 1 residues within 4Å: Chain D: E.11 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.11, D:E.11, H2O.15 ZN.17: 3 residues within 4Å: Chain A: E.70, D.71 Chain E: E.122 5 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: E:E.122, E:E.122, A:D.71, A:D.71, H2O.4 ZN.18: 2 residues within 4Å: Chain E: D.143, E.147 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.143, E:D.143, E:E.147 ZN.19: 4 residues within 4Å: Chain E: H.82 Chain F: R.13 Chain G: D.134 Ligands: ZN.20 5 PLIP interactions: 2 interactions with chain G, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: G:D.134, G:D.134, E:H.82, H2O.20, H2O.23 ZN.20: 3 residues within 4Å: Chain E: H.82 Chain G: D.134 Ligands: ZN.19 5 PLIP interactions: 2 interactions with chain G, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: G:D.134, G:D.134, E:H.82, H2O.20, H2O.20 ZN.21: 4 residues within 4Å: Chain E: C.116, I.117 Ligands: ZN.6, ZN.22 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:C.116, H2O.20, H2O.20, H2O.20 ZN.22: 6 residues within 4Å: Chain A: C.116, E.118 Chain E: C.116 Ligands: ZN.5, ZN.6, ZN.21 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: A:C.116, E:C.116, H2O.5, H2O.20 ZN.24: 1 residues within 4Å: Chain F: E.11 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.11, F:E.11, H2O.23 ZN.25: 3 residues within 4Å: Chain C: E.70, D.71 Chain G: E.122 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: C:D.71, C:D.71, G:E.122, G:E.122, H2O.12 ZN.26: 2 residues within 4Å: Chain G: D.143, E.147 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:D.143, G:D.143, G:E.147 ZN.27: 4 residues within 4Å: Chain E: D.134 Chain G: H.82 Chain H: R.13 Ligands: ZN.28 5 PLIP interactions: 1 interactions with chain G, 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: G:H.82, E:D.134, E:D.134, H2O.28, H2O.31 ZN.28: 3 residues within 4Å: Chain E: D.134 Chain G: H.82 Ligands: ZN.27 5 PLIP interactions: 1 interactions with chain G, 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: G:H.82, E:D.134, E:D.134, H2O.28, H2O.28 ZN.29: 4 residues within 4Å: Chain G: C.116, I.117 Ligands: ZN.14, ZN.30 4 PLIP interactions: 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:C.116, H2O.28, H2O.28, H2O.28 ZN.30: 6 residues within 4Å: Chain C: C.116, E.118 Chain G: C.116 Ligands: ZN.13, ZN.14, ZN.29 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: C:C.116, G:C.116, H2O.13, H2O.28 ZN.32: 1 residues within 4Å: Chain H: E.11 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.11, H:E.11, H2O.31

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

CL.7: 5 residues within 4Å: Chain A: I.81, R.130 Chain C: I.81, R.130 Ligands: CL.15 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain A: I.81, R.130 Chain C: I.81, R.130 Ligands: CL.7 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain E: I.81, R.130 Chain G: I.81, R.130 Ligands: CL.31 Ligand excluded by PLIP CL.31: 5 residues within 4Å: Chain E: I.81, R.130 Chain G: I.81, R.130 Ligands: CL.23 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: 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

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

Bcl-2-like protein 11

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