SMTL ID : 2cdr.1

Crystal structures of caspase-3 in complex with aza-peptide epoxide inhibitors.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-4-4-mer

Ligands

4 x PHQ- ASP- GLU- VAL- MY1: AZA-PEPTIDE EXPOXIDE(Non-covalent)

PHQ-ASP-GLU-VAL-MY1.1: 27 residues within 4Å: Chain A: M.33, R.36, S.37, S.92, H.93, G.94, E.95, F.100, Q.133, A.134, C.135, G.137, T.138 Chain B: Y.30, S.31, W.32, R.33, N.34, S.35, W.40, E.74, S.75, F.76, F.78, F.82 Chain D: D.5 Chain E: E.95 34 PLIP interactions: 18 interactions with chain B, 15 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: B:Y.30, B:W.32, B:W.32, B:F.76, B:F.78, B:F.82, A:M.33, A:H.93, A:E.95, A:E.95, A:T.138 Hydrogen bonds: B:S.31, B:R.33, B:R.33, B:R.33, B:N.34, B:S.35, B:F.76, B:F.76, B:F.76, A:S.37, A:S.37, A:H.93, A:G.94, A:Q.133, A:C.135, D:D.5 Water bridges: B:K.36 Salt bridges: B:R.33, B:R.33, A:R.36, A:H.93 pi-Stacking: A:H.93, A:F.100 PHQ-ASP-GLU-VAL-MY1.2: 27 residues within 4Å: Chain B: D.5 Chain C: M.33, R.36, S.37, S.92, H.93, G.94, E.95, F.100, Q.133, A.134, C.135, G.137, T.138 Chain D: Y.30, S.31, W.32, R.33, N.34, S.35, W.40, E.74, S.75, F.76, F.78, F.82 Chain G: E.95 33 PLIP interactions: 15 interactions with chain C, 18 interactions with chain D Hydrophobic interactions: C:M.33, C:H.93, C:E.95, C:E.95, C:T.138, D:Y.30, D:W.32, D:W.32, D:F.76, D:F.78, D:F.82 Hydrogen bonds: C:S.37, C:S.37, C:H.93, C:G.94, C:Q.133, C:C.135, D:S.31, D:R.33, D:R.33, D:R.33, D:R.33, D:N.34, D:S.35, D:F.76, D:F.76 Salt bridges: C:R.36, C:H.93, D:R.33, D:R.33 pi-Stacking: C:H.93, C:F.100 Water bridges: D:K.36 PHQ-ASP-GLU-VAL-MY1.3: 27 residues within 4Å: Chain A: E.95 Chain E: M.33, R.36, S.37, S.92, H.93, G.94, E.95, F.100, Q.133, A.134, C.135, G.137, T.138 Chain F: Y.30, S.31, W.32, R.33, N.34, S.35, W.40, E.74, S.75, F.76, F.78, F.82 Chain H: D.5 34 PLIP interactions: 15 interactions with chain E, 18 interactions with chain F, 1 interactions with chain H Hydrophobic interactions: E:M.33, E:H.93, E:E.95, E:E.95, E:T.138, F:Y.30, F:W.32, F:W.32, F:F.76, F:F.78, F:F.82 Hydrogen bonds: E:S.37, E:S.37, E:H.93, E:G.94, E:Q.133, E:C.135, F:S.31, F:R.33, F:R.33, F:R.33, F:N.34, F:S.35, F:F.76, F:F.76, F:F.76, H:D.5 Salt bridges: E:R.36, E:H.93, F:R.33, F:R.33 pi-Stacking: E:H.93, E:F.100 Water bridges: F:K.36 PHQ-ASP-GLU-VAL-MY1.4: 27 residues within 4Å: Chain C: E.95 Chain F: D.5 Chain G: M.33, R.36, S.37, S.92, H.93, G.94, E.95, F.100, Q.133, A.134, C.135, G.137, T.138 Chain H: Y.30, S.31, W.32, R.33, N.34, S.35, W.40, E.74, S.75, F.76, F.78, F.82 33 PLIP interactions: 18 interactions with chain H, 15 interactions with chain G Hydrophobic interactions: H:Y.30, H:W.32, H:W.32, H:F.76, H:F.78, H:F.82, G:M.33, G:H.93, G:E.95, G:E.95, G:T.138 Hydrogen bonds: H:S.31, H:R.33, H:R.33, H:R.33, H:R.33, H:N.34, H:S.35, H:F.76, H:F.76, G:S.37, G:S.37, G:H.93, G:G.94, G:Q.133, G:C.135 Water bridges: H:K.36 Salt bridges: H:R.33, H:R.33, G:R.36, G:H.93 pi-Stacking: G:H.93, G:F.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ganesan, R. et al., Exploring the S4 and S1 Prime Subsite Specificities in Caspase-3 with Aza-Peptide Epoxide Inhibitors. Biochemistry (2006)

Release Date

2007-03-20

Peptides

CASPASE-3 SUBUNIT P17: ACEG
CASPASE-3 SUBUNIT P12: 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

CASPASE-3 SUBUNIT P17

CASPASE-3 SUBUNIT P12

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