SMTL ID : 2oaf.1

Crystal structure of thioesterase superfamily (YP_508616.1) from Jannaschia sp. CCS1 at 2.00 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 7 residues within 4Å: Chain A: G.37, H.38, R.41 Chain B: G.37, H.38, R.41 Ligands: PO4.10 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:G.37, B:G.37 Salt bridges: B:H.38, B:R.41, A:H.38, A:R.41 Water bridges: A:R.41, A:R.41, A:R.41 PO4.2: 7 residues within 4Å: Chain A: D.29, I.33, A.34, Y.35, T.36 Chain B: P.72, F.73 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:F.73, A:D.29, A:T.36, A:T.36, A:T.36 Water bridges: A:A.34 PO4.6: 5 residues within 4Å: Chain B: R.98, G.100, T.101, K.102, S.103 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.100, B:T.101, B:K.102, B:S.103, B:S.103 Water bridges: B:R.98, B:T.101 Salt bridges: B:R.98 PO4.10: 7 residues within 4Å: Chain C: G.37, H.38, R.41 Chain D: G.37, H.38, R.41 Ligands: PO4.1 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain D Water bridges: C:R.41, C:R.41, C:R.41 Salt bridges: C:H.38, C:R.41, D:H.38, D:R.41 Hydrogen bonds: D:G.37, D:G.37 PO4.11: 7 residues within 4Å: Chain C: D.29, I.33, A.34, Y.35, T.36 Chain D: P.72, F.73 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:D.29, C:D.29, C:T.36, C:T.36, C:T.36, C:T.36, D:F.73 Water bridges: C:A.34 PO4.15: 5 residues within 4Å: Chain D: R.98, G.100, T.101, K.102, S.103 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:G.100, D:T.101, D:K.102, D:S.103, D:S.103 Water bridges: D:R.98, D:R.98 Salt bridges: D:R.98

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

CL.3: 2 residues within 4Å: Chain A: H.55, H.140 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain C: H.55, H.140 Ligand excluded by PLIP

4 x CIT: CITRIC ACID(Non-functional Binders)

CIT.4: 5 residues within 4Å: Chain A: R.98, G.100, T.101, K.102, S.103 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.101, A:T.101, A:K.102, A:S.103 Salt bridges: A:R.98, A:R.98 CIT.5: 4 residues within 4Å: Chain A: H.88, I.89, K.91, D.113 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.89 Water bridges: A:D.113 Salt bridges: A:H.88, A:H.88, A:K.91 CIT.13: 5 residues within 4Å: Chain C: R.98, G.100, T.101, K.102, S.103 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.101, C:T.101, C:K.102, C:S.103 Salt bridges: C:R.98, C:R.98 CIT.14: 4 residues within 4Å: Chain C: H.88, I.89, K.91, D.113 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:I.89, C:D.113 Water bridges: C:D.113 Salt bridges: C:H.88, C:H.88, C:K.91

6 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 9 residues within 4Å: Chain A: I.33, F.80, K.81, S.82, P.83 Chain B: V.125, T.127, F.132, S.134 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.132 PGE.8: 10 residues within 4Å: Chain A: P.72, F.73, V.74, V.125, F.132, S.134 Chain B: F.80, K.81, S.82, P.83 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:S.82, A:S.134, A:S.134 PGE.9: 6 residues within 4Å: Chain B: D.14, S.15, A.16, F.17, V.18, Y.54 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.54 PGE.16: 9 residues within 4Å: Chain C: I.33, F.80, K.81, S.82, P.83 Chain D: V.125, T.127, F.132, S.134 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:F.132 PGE.17: 10 residues within 4Å: Chain C: P.72, F.73, V.74, V.125, F.132, S.134 Chain D: F.80, K.81, S.82, P.83 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Water bridges: D:S.82, C:S.134, C:S.134 PGE.18: 6 residues within 4Å: Chain D: D.14, S.15, A.16, F.17, V.18, Y.54 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of thioesterase superfamily (YP_508616.1) from Jannaschia sp. CCS1 at 2.00 A resolution. To be published

Release Date

2007-02-13

Peptides

Thioesterase superfamily: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Thioesterase superfamily