SMTL ID : 1xb0.1

Structure of the BIR domain of IAP-like protein 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

6 x ALA- VAL- PRO- ILE: Diablo homolog, mitochondrial(Non-covalent)

ALA-VAL-PRO-ILE.1: 11 residues within 4Å: Chain A: K.49, G.58, L.59, A.60, N.61, W.62, E.66, Q.71, W.75, Y.76 Chain F: I.22 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain F Hydrophobic interactions: A:K.49, A:A.60, A:W.62, A:W.75, F:I.22 Hydrogen bonds: A:G.58, A:A.60, A:A.60, A:E.66 Water bridges: A:G.58, A:Q.71, A:Q.71 ALA-VAL-PRO-ILE.2: 12 residues within 4Å: Chain A: I.22 Chain B: K.49, V.50, G.58, L.59, A.60, N.61, W.62, E.66, Q.71, W.75, Y.76 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.49, B:A.60, B:W.62, B:W.75, A:I.22 Hydrogen bonds: B:G.58, B:A.60, B:A.60, B:E.66 Water bridges: B:G.58, B:Q.71, B:Q.71 ALA-VAL-PRO-ILE.3: 12 residues within 4Å: Chain B: I.22 Chain C: K.49, V.50, G.58, L.59, A.60, N.61, W.62, E.66, Q.71, W.75, Y.76 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:K.49, C:W.62 Hydrogen bonds: C:G.58, C:A.60, C:A.60, C:Q.71 Water bridges: C:Q.71 ALA-VAL-PRO-ILE.4: 11 residues within 4Å: Chain C: I.22 Chain D: K.49, G.58, L.59, A.60, N.61, W.62, E.66, Q.71, W.75, Y.76 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:K.49, D:A.60, D:W.62, C:I.22 Hydrogen bonds: D:G.58, D:A.60, D:A.60, D:E.66 Water bridges: D:G.58, D:Q.71, D:K.74 ALA-VAL-PRO-ILE.5: 12 residues within 4Å: Chain D: I.22 Chain E: K.49, V.50, G.58, L.59, A.60, N.61, W.62, E.66, Q.71, W.75, Y.76 12 PLIP interactions: 11 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:K.49, E:A.60, E:W.62, E:W.75, D:I.22 Hydrogen bonds: E:G.58, E:A.60, E:A.60, E:E.66 Water bridges: E:G.58, E:Q.71, E:K.74 ALA-VAL-PRO-ILE.6: 12 residues within 4Å: Chain E: I.22 Chain F: K.49, V.50, G.58, L.59, A.60, N.61, W.62, E.66, Q.71, W.75, Y.76 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:K.49, F:W.62, F:W.75 Hydrogen bonds: F:G.58, F:A.60, F:A.60, F:E.66 Water bridges: F:Q.71

24 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain A: C.52, C.55, H.72, C.79 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.52, A:C.55, A:H.72, A:C.79 ZN.8: 2 residues within 4Å: Chain A: H.54, E.84 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.54, A:E.84, A:E.84, H2O.2 ZN.9: 2 residues within 4Å: Chain A: E.85 Chain B: L.104 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.85, A:E.85, H2O.2, H2O.4 ZN.10: 2 residues within 4Å: Chain A: H.95 Chain F: E.18 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: A:H.95, F:E.18, H2O.2, H2O.11 ZN.11: 3 residues within 4Å: Chain A: E.18 Chain B: H.95, T.108 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.95, B:T.108, A:E.18, H2O.4 ZN.12: 1 residues within 4Å: Chain B: E.85 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.85 ZN.13: 2 residues within 4Å: Chain B: H.54, E.84 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.54, B:E.84, B:E.84 ZN.14: 4 residues within 4Å: Chain B: C.52, C.55, H.72, C.79 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.52, B:C.55, B:H.72, B:C.79 ZN.15: 2 residues within 4Å: Chain B: E.18 Chain C: H.95 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:H.95, B:E.18, H2O.5, H2O.6 ZN.16: 1 residues within 4Å: Chain C: E.85 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.85, C:E.85, H2O.5 ZN.17: 2 residues within 4Å: Chain C: H.54, E.84 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.54, C:E.84, C:E.84, H2O.6 ZN.18: 4 residues within 4Å: Chain C: C.52, C.55, H.72, C.79 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.52, C:C.55, C:H.72, C:C.79 ZN.19: 2 residues within 4Å: Chain C: E.18 Chain D: H.95 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:E.18, D:H.95, H2O.6, H2O.8 ZN.20: 1 residues within 4Å: Chain D: E.85 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.85 ZN.21: 2 residues within 4Å: Chain D: H.54, E.84 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.54, D:E.84, D:E.84, H2O.7 ZN.22: 4 residues within 4Å: Chain D: C.52, C.55, H.72, C.79 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.52, D:C.55, D:H.72, D:C.79 ZN.23: 2 residues within 4Å: Chain D: E.18 Chain E: H.95 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: D:E.18, D:E.18, E:H.95, H2O.8, H2O.10 ZN.24: 3 residues within 4Å: Chain E: E.85 Chain F: L.104, Q.106 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.85, E:E.85, H2O.10 ZN.25: 2 residues within 4Å: Chain E: H.54, E.84 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.54, E:E.84, E:E.84, H2O.10 ZN.26: 4 residues within 4Å: Chain E: C.52, C.55, H.72, C.79 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.52, E:C.55, E:H.72, E:C.79 ZN.27: 3 residues within 4Å: Chain E: E.18 Chain F: H.95, T.108 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Metal complexes: F:H.95, F:T.108, E:E.18 ZN.28: 1 residues within 4Å: Chain F: E.85 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.85, F:E.85, H2O.12 ZN.29: 2 residues within 4Å: Chain F: H.54, E.84 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.54, F:E.84 ZN.30: 4 residues within 4Å: Chain F: C.52, C.55, H.72, C.79 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.52, F:C.55, F:H.72, F:C.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shin, H. et al., The BIR domain of IAP-like protein 2 is conformationally unstable: implications for caspase inhibition. Biochem.J. (2005)

Release Date

2004-11-02

Peptides

Baculoviral IAP repeat-containing protein 8: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Baculoviral IAP repeat-containing protein 8

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