SMTL ID : 4quh.1

Caspase-3 T140G

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-dimer

Ligands

1 x GLY- VAL- ASP- ASP- ASP: short peptde(Non-covalent)

GLY-VAL-ASP-ASP-ASP.1: 6 residues within 4Å: Chain A: R.75, V.85, R.86, N.87, K.88, N.89 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:N.87 Hydrogen bonds: A:N.87, A:N.87, A:N.87, A:N.87 Water bridges: A:R.75, A:K.88 Salt bridges: A:R.75

2 x ACE- ASP- GLU- VAL- ASP- 0QE: ACE-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE INHIBITOR(Non-covalent)

ACE-ASP-GLU-VAL-ASP-0QE.2: 16 residues within 4Å: Chain B: R.64, S.120, H.121, G.122, Q.161, C.163, Y.204, S.205, W.206, R.207, N.208, S.209, W.214, E.248, S.249, F.250 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:H.121, B:Y.204, B:Y.204, B:W.206, B:W.206 Hydrogen bonds: B:H.121, B:Q.161, B:S.205, B:R.207, B:R.207, B:R.207, B:N.208, B:S.209, B:F.250, B:F.250 Water bridges: B:S.65, B:R.207, B:S.209, B:S.209, B:F.250, B:F.250 Salt bridges: B:R.64, B:R.207, B:R.207 ACE-ASP-GLU-VAL-ASP-0QE.3: 17 residues within 4Å: Chain A: R.64, S.120, H.121, G.122, Q.161, C.163, Y.204, S.205, W.206, R.207, N.208, S.209, W.214, E.248, S.249, F.250, F.256 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:H.121, A:Y.204, A:Y.204, A:W.206, A:W.206, A:F.256 Hydrogen bonds: A:Q.161, A:S.205, A:R.207, A:R.207, A:R.207, A:N.208, A:S.209, A:F.250 Water bridges: A:S.209, A:S.209, A:F.250, A:F.250 Salt bridges: A:R.64, A:H.121, A:R.207, A:R.207

2 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.4: 7 residues within 4Å: Chain A: L.136, K.137, Y.195, Y.197, V.266, M.268 Chain B: P.201 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.137, A:Y.195, A:V.266, B:P.201 Hydrogen bonds: A:L.136, A:Y.197 Water bridges: A:R.164 MRD.7: 7 residues within 4Å: Chain A: P.201 Chain B: L.136, K.137, Y.195, Y.197, V.266, M.268 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.137, B:Y.195, B:Y.195, B:V.266, A:P.201 Hydrogen bonds: B:L.136, B:Y.197 Water bridges: B:Y.197

4 x AZI: AZIDE ION(Non-covalent)

AZI.5: 5 residues within 4Å: Chain A: K.53, G.66, T.67, D.68, V.69 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.53, A:G.66, A:T.67, A:D.68, A:V.69 AZI.6: 5 residues within 4Å: Chain A: N.73, T.77, C.220, A.221, K.224 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.73, A:N.73 Water bridges: A:A.221, A:A.221 AZI.8: 5 residues within 4Å: Chain B: K.53, G.66, T.67, D.68, V.69 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.66, B:T.67, B:D.68, B:D.68, B:V.69 AZI.9: 4 residues within 4Å: Chain B: N.80, L.81, A.227, F.275 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.80, B:F.275

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.10: 5 residues within 4Å: Chain B: R.75, V.85, R.86, N.87, N.89 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cade, C. et al., Modifying caspase-3 activity by altering allosteric networks. Biochemistry (2014)

Release Date

2014-11-05

Peptides

Caspase-3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Caspase-3