SMTL ID : 6bdv.2 (2 other biounits)

Crystal structure of Caspase 3 S150A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

hetero-4-4-mer

Ligands

4 x ACE- ASP- GLU- VAL- ASP- 0QE: Acetyl-Asp-Glu-Val-Asp-CMK(Non-covalent)

ACE-ASP-GLU-VAL-ASP-0QE.1: 17 residues within 4Å: Chain A: R.64, S.120, H.121, Q.161, A.162, C.163 Chain B: Y.29, S.30, W.31, R.32, N.33, S.34, W.39, E.73, S.74, F.75 Chain C: S.58 19 PLIP interactions: 5 interactions with chain A, 14 interactions with chain B Hydrogen bonds: A:Q.161, A:C.163, B:S.30, B:R.32, B:R.32, B:N.33, B:S.34, B:F.75 Water bridges: A:G.122, B:F.75 Salt bridges: A:R.64, A:H.121, B:R.32, B:R.32 Hydrophobic interactions: B:Y.29, B:Y.29, B:W.31, B:W.31, B:R.32 ACE-ASP-GLU-VAL-ASP-0QE.5: 17 residues within 4Å: Chain A: S.58 Chain C: R.64, S.120, H.121, Q.161, A.162, C.163 Chain D: Y.29, S.30, W.31, R.32, N.33, S.34, W.39, E.73, S.74, F.75 19 PLIP interactions: 5 interactions with chain C, 14 interactions with chain D Hydrogen bonds: C:Q.161, C:C.163, D:S.30, D:R.32, D:R.32, D:N.33, D:S.34, D:F.75 Water bridges: C:G.122, D:F.75 Salt bridges: C:R.64, C:H.121, D:R.32, D:R.32 Hydrophobic interactions: D:Y.29, D:Y.29, D:W.31, D:W.31, D:R.32 ACE-ASP-GLU-VAL-ASP-0QE.9: 17 residues within 4Å: Chain E: R.64, S.120, H.121, Q.161, A.162, C.163 Chain F: Y.29, S.30, W.31, R.32, N.33, S.34, W.39, E.73, S.74, F.75 Chain G: S.58 22 PLIP interactions: 7 interactions with chain E, 15 interactions with chain F Hydrogen bonds: E:H.121, E:Q.161, E:C.163, F:S.30, F:R.32, F:R.32, F:N.33, F:S.34, F:F.75, F:F.75 Water bridges: E:T.62, E:G.122, F:F.75 Salt bridges: E:R.64, E:H.121, F:R.32, F:R.32 Hydrophobic interactions: F:Y.29, F:Y.29, F:W.31, F:W.31, F:R.32 ACE-ASP-GLU-VAL-ASP-0QE.13: 17 residues within 4Å: Chain E: S.58 Chain G: R.64, S.120, H.121, Q.161, A.162, C.163 Chain H: Y.29, S.30, W.31, R.32, N.33, S.34, W.39, E.73, S.74, F.75 22 PLIP interactions: 15 interactions with chain H, 7 interactions with chain G Hydrophobic interactions: H:Y.29, H:Y.29, H:W.31, H:W.31, H:R.32 Hydrogen bonds: H:S.30, H:R.32, H:R.32, H:N.33, H:S.34, H:F.75, H:F.75, G:H.121, G:Q.161, G:C.163 Water bridges: H:F.75, G:T.62, G:G.122 Salt bridges: H:R.32, H:R.32, G:R.64, G:H.121

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

CL.2: 5 residues within 4Å: Chain A: K.53, S.65, G.66, T.67, D.68 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain C: K.53, S.65, G.66, T.67, D.68 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain E: K.53, S.65, G.66, T.67, D.68 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain G: K.53, S.65, G.66, T.67, D.68 Ligand excluded by PLIP

8 x AZI: AZIDE ION(Non-covalent)

AZI.3: 3 residues within 4Å: Chain A: T.92, E.94, E.95 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.92, A:E.94, A:E.94 AZI.4: 3 residues within 4Å: Chain A: S.36 Chain B: Y.99, Y.101 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.99, B:Y.101, A:S.36 AZI.7: 3 residues within 4Å: Chain C: T.92, E.94, E.95 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.94, C:E.94 AZI.8: 3 residues within 4Å: Chain C: S.36 Chain D: Y.99, Y.101 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:S.36, D:Y.101, D:Y.101 AZI.11: 3 residues within 4Å: Chain E: T.92, E.94, E.95 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.92 AZI.12: 3 residues within 4Å: Chain E: S.36 Chain F: Y.99, Y.101 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:S.36, F:Y.99 AZI.15: 3 residues within 4Å: Chain G: T.92, E.94, E.95 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:T.92, G:T.92 AZI.16: 3 residues within 4Å: Chain G: S.36 Chain H: Y.99, Y.101 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:S.36, G:S.36, H:Y.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thomas, M.E. et al., Modifications to a common phosphorylation network provide individualized control in caspases. J. Biol. Chem. (2018)

Release Date

2018-02-14

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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