SMTL ID : 3f5o.1 (1 other biounit)

Crystal Structure of hTHEM2(undecan-2-one-CoA) complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

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

CL.1: 5 residues within 4Å: Chain A: N.50, H.56, G.57 Ligands: UOC.4, COA.5 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain C: N.50, H.56, G.57 Ligands: UOC.12, COA.13 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain D: N.50, H.56, G.57 Ligands: UOC.8, COA.9 Ligand excluded by PLIP

4 x UOC: undecan-2-one(Non-covalent)

UOC.2: 11 residues within 4Å: Chain A: M.15, N.66, T.69, M.70, L.73, G.81, V.82, S.83, K.136 Chain B: N.50 Ligands: COA.3 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.50 Hydrophobic interactions: A:T.69, A:L.73 UOC.4: 11 residues within 4Å: Chain A: N.50, A.51 Chain B: L.73, P.80, G.81, V.82, S.83, K.136 Ligands: CL.1, COA.5, P6G.6 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.80, B:V.82, A:A.51 Hydrogen bonds: B:S.83, B:K.136 Water bridges: A:G.57 UOC.8: 11 residues within 4Å: Chain C: L.73, G.81, V.82, S.83, K.136 Chain D: N.50, A.51, I.52 Ligands: COA.9, P6G.10, CL.11 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:A.51, D:I.52, C:L.73 Hydrogen bonds: C:S.83, C:K.136 Water bridges: C:T.69 UOC.12: 7 residues within 4Å: Chain C: N.50, I.52 Chain D: G.81, V.82, K.136 Ligands: CL.7, COA.13 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.83, D:K.136 Hydrophobic interactions: C:I.52

4 x COA: COENZYME A(Non-covalent)

COA.3: 16 residues within 4Å: Chain A: V.82, S.83, H.137, G.139 Chain B: L.55, Y.90, M.91, S.92, P.93 Chain C: K.108, G.110, K.111, T.112, L.113, F.115 Ligands: UOC.2 15 PLIP interactions: 8 interactions with chain C, 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: C:F.115, B:Y.90 Hydrogen bonds: C:K.111, C:T.112, C:L.113, A:S.83, A:S.83, A:H.137, B:Y.90 Water bridges: C:Q.109, C:G.110, B:T.54 Salt bridges: C:K.108, C:K.111, A:H.137 COA.5: 19 residues within 4Å: Chain A: N.50, L.55, Y.90, M.91, S.92, P.93, K.95 Chain B: V.82, S.83, H.137, G.139 Chain D: K.108, G.110, K.111, T.112, L.113, F.115 Ligands: CL.1, UOC.4 16 PLIP interactions: 6 interactions with chain D, 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: D:L.113, B:H.137, A:Y.90 Hydrogen bonds: D:K.111, D:T.112, D:L.113, B:S.83, B:S.83, A:Y.90 Water bridges: D:K.108, B:H.137, A:S.92, A:A.94 Salt bridges: D:K.108, B:H.137, B:H.137 COA.9: 20 residues within 4Å: Chain A: K.108, G.110, K.111, T.112, L.113, F.115 Chain C: V.82, S.83, V.84, H.137, G.139 Chain D: N.50, L.55, Y.90, M.91, S.92, P.93, K.95 Ligands: UOC.8, CL.11 18 PLIP interactions: 3 interactions with chain D, 7 interactions with chain A, 8 interactions with chain C Hydrogen bonds: D:Y.90, D:K.95, A:K.111, A:T.112, A:L.113, C:S.83, C:S.83 Water bridges: D:S.92, A:K.108, C:H.137 Hydrophobic interactions: A:L.113, C:V.82, C:V.84, C:H.137 Salt bridges: A:K.108, A:K.108, C:H.137, C:H.137 COA.13: 17 residues within 4Å: Chain B: K.108, G.110, K.111, T.112, L.113, F.115 Chain C: L.55, Y.90, M.91, S.92, P.93, K.95 Chain D: V.82, S.83, H.137 Ligands: CL.7, UOC.12 18 PLIP interactions: 6 interactions with chain D, 7 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: D:V.82, D:H.137, B:L.113 Hydrogen bonds: D:S.83, D:S.83, B:K.111, B:T.112, B:L.113, C:Y.90, C:K.95, C:K.95 Salt bridges: D:H.137, D:H.137, B:K.108, B:K.108 Water bridges: B:K.108, C:S.92, C:A.94

2 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.6: 10 residues within 4Å: Chain A: A.51 Chain B: V.11, M.15, N.20, E.22, N.66, T.69, M.70, L.73 Ligands: UOC.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.20 P6G.10: 13 residues within 4Å: Chain C: V.11, A.14, M.15, K.17, A.18, N.20, E.22, N.66, T.69, M.70, L.73 Chain D: A.51 Ligands: UOC.8 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.20 Water bridges: C:T.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, J. et al., The mechanisms of human hotdog-fold thioesterase 2 (hTHEM2) substrate recognition and catalysis illuminated by a structure and function based analysis. Biochemistry (2009)

Release Date

2009-08-18

Peptides

Thioesterase superfamily member 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Thioesterase superfamily member 2

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