SMTL ID : 3vpt.1

Crystal structure of Bombyx mori sigma-class glutathione transferase in apo form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

12 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.1: 6 residues within 4Å: Chain A: K.132 Chain B: P.44, T.46, P.47, F.48, G.49 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.46, B:G.49, A:K.132 PGO.2: 2 residues within 4Å: Chain A: K.12, A.157 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.12, A:K.12 PGO.3: 5 residues within 4Å: Chain A: Y.7, K.45, V.53, E.55, Q.60 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.7, A:E.55, A:Q.60 PGO.4: 2 residues within 4Å: Chain A: R.73 Chain B: D.82 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.73 PGO.8: 6 residues within 4Å: Chain A: G.76, L.77, A.78, G.79, K.148, L.149 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.79, A:L.149 Water bridges: A:A.78 PGO.9: 5 residues within 4Å: Chain A: T.65, V.92, N.96, R.99, V.155 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.155 Hydrogen bonds: A:T.65, A:V.92, A:N.96 PGO.12: 6 residues within 4Å: Chain A: P.44, T.46, P.47, F.48, G.49 Chain B: K.132 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.132, A:T.46, A:G.49 PGO.13: 2 residues within 4Å: Chain B: K.12, A.157 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.12, B:K.12 PGO.14: 5 residues within 4Å: Chain B: Y.7, K.45, V.53, E.55, Q.60 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.7, B:E.55, B:Q.60 PGO.15: 2 residues within 4Å: Chain A: D.82 Chain B: R.73 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.73 PGO.19: 6 residues within 4Å: Chain B: G.76, L.77, A.78, G.79, K.148, L.149 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.79, B:L.149 Water bridges: B:A.78 PGO.20: 5 residues within 4Å: Chain B: T.65, V.92, N.96, R.99, V.155 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.155 Hydrogen bonds: B:V.92, B:N.96

8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 4 residues within 4Å: Chain A: P.127, E.131, K.175, Y.176 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.175 PEG.6: 4 residues within 4Å: Chain A: N.141, G.142, A.178, K.181 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.141 PEG.7: 6 residues within 4Å: Chain A: E.87, Q.90, N.91, E.135, K.139, N.140 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.87, A:Q.90, A:N.91, A:N.140 PEG.11: 1 residues within 4Å: Chain A: N.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.141 PEG.16: 4 residues within 4Å: Chain B: P.127, E.131, K.175, Y.176 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.175, B:Y.176 PEG.17: 4 residues within 4Å: Chain B: N.141, G.142, A.178, K.181 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.141 PEG.18: 6 residues within 4Å: Chain B: E.87, Q.90, N.91, E.135, K.139, N.140 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.87, B:Q.90, B:N.91, B:N.140 PEG.22: 1 residues within 4Å: Chain B: N.141 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.141

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.10: 6 residues within 4Å: Chain A: D.97, S.101, S.104, L.121, K.125 Chain B: Q.50 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.104, A:K.125, B:Q.50 PG4.21: 6 residues within 4Å: Chain A: Q.50 Chain B: D.97, S.101, S.104, L.121, K.125 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.104, B:K.125, A:Q.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamamoto, K. et al., Crystal structure of a Bombyx mori sigma-class glutathione transferase exhibiting prostaglandin E synthase activity. Biochim.Biophys.Acta (2013)

Release Date

2013-03-06

Peptides

Glutathione S-transferase sigma: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutathione S-transferase sigma

Related Entries With Identical Sequence