SMTL ID : 5szy.2 (1 other biounit)

Novel Structural Insights into GDP-Mediated Regulation of Acyl-CoA Thioesterases

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

6 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 13 residues within 4Å: Chain A: E.14, Y.80, A.81, A.82, N.84, G.94, I.95, R.96, H.109, S.112, Y.114, R.141 Chain D: R.8 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:A.81, A:A.82, A:N.84, A:N.84, A:G.94, A:S.112, D:R.8 Water bridges: A:E.14, A:E.14, A:S.112, A:Y.114, A:Y.114 Salt bridges: A:E.14, A:R.96, A:H.109 GDP.5: 14 residues within 4Å: Chain B: E.14, Y.80, A.81, A.82, N.84, G.94, I.95, R.96, H.109, S.112, Y.114, R.141, K.144 Chain E: R.8 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:A.81, B:A.82, B:N.84, B:N.84, B:G.94, B:S.112, B:Y.114, B:R.141, E:R.8 Water bridges: B:E.14, B:Y.114, B:R.141, B:R.141, B:K.144, B:R.148 Salt bridges: B:E.14, B:R.96, B:H.109, B:R.141, B:K.144 pi-Cation interactions: B:R.141 GDP.7: 13 residues within 4Å: Chain C: E.14, Y.80, A.81, A.82, N.84, G.94, I.95, R.96, H.109, S.112, Y.114, R.141 Chain F: R.8 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:A.81, C:A.82, C:N.84, C:N.84, C:G.94, C:S.112, C:Y.114, F:R.8 Water bridges: C:E.14, C:S.112 Salt bridges: C:E.14, C:R.96, C:H.109 GDP.11: 14 residues within 4Å: Chain A: R.8 Chain D: E.14, Y.80, A.81, A.82, N.84, G.94, I.95, R.96, H.109, S.112, Y.114, R.141, K.144 22 PLIP interactions: 21 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:A.81, D:A.82, D:N.84, D:N.84, D:G.94, D:S.112, D:R.141, A:R.8 Water bridges: D:E.14, D:Y.114, D:Y.114, D:Y.114, D:R.141, D:R.141, D:K.144, D:R.148 Salt bridges: D:E.14, D:R.96, D:H.109, D:R.141, D:K.144 pi-Cation interactions: D:R.141 GDP.13: 13 residues within 4Å: Chain B: R.8 Chain E: E.14, Y.80, A.81, A.82, N.84, G.94, I.95, R.96, H.109, S.112, Y.114, R.141 14 PLIP interactions: 13 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:A.81, E:A.82, E:N.84, E:N.84, E:G.94, E:S.112, E:Y.114, B:R.8 Water bridges: E:E.14, E:E.14, E:S.112 Salt bridges: E:E.14, E:R.96, E:H.109 GDP.17: 14 residues within 4Å: Chain C: R.8 Chain F: E.14, Y.80, A.81, A.82, N.84, G.94, I.95, R.96, H.109, S.112, Y.114, R.141, K.144 23 PLIP interactions: 22 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:A.81, F:A.82, F:N.84, F:N.84, F:G.94, F:S.112, F:R.141, C:R.8 Water bridges: F:E.14, F:E.14, F:Y.114, F:Y.114, F:Y.114, F:R.141, F:R.141, F:K.144, F:R.148 Salt bridges: F:E.14, F:R.96, F:H.109, F:R.141, F:K.144 pi-Cation interactions: F:R.141

6 x COA: COENZYME A(Non-covalent)

COA.2: 20 residues within 4Å: Chain A: V.58, T.59, L.60, G.87, R.88, T.89, S.90, V.118, P.125, R.149, S.152 Chain B: V.32, G.34, L.37, L.66, F.67, K.68, E.69, P.70 Ligands: CL.3 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:T.59, A:R.88, A:R.88, A:T.89, A:S.90, A:S.90, A:R.149, B:F.67, B:K.68 Salt bridges: A:R.149, B:K.68 Water bridges: B:I.71 COA.6: 21 residues within 4Å: Chain A: V.32, G.34, L.37, L.66, F.67, K.68, E.69, P.70 Chain B: V.58, T.59, L.60, G.87, R.88, T.89, S.90, V.118, P.125, R.149, S.152, L.153 Ligands: CL.4 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.59, B:R.88, B:T.89, B:S.90, B:S.90, B:R.149, B:R.149, B:S.152, A:F.67, A:K.68 Water bridges: B:R.88, B:R.88 Salt bridges: B:R.149, A:K.68 COA.8: 20 residues within 4Å: Chain C: V.58, T.59, L.60, G.87, R.88, T.89, S.90, V.118, P.125, R.149, S.152 Chain D: V.32, G.34, L.37, L.66, F.67, K.68, E.69, P.70 Ligands: CL.9 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:T.59, C:R.88, C:R.88, C:T.89, C:S.90, C:S.90, C:R.149, D:F.67, D:K.68 Salt bridges: C:R.149, D:K.68 Water bridges: D:I.71 COA.12: 21 residues within 4Å: Chain C: V.32, G.34, L.37, L.66, F.67, K.68, E.69, P.70 Chain D: V.58, T.59, L.60, G.87, R.88, T.89, S.90, V.118, P.125, R.149, S.152, L.153 Ligands: CL.10 14 PLIP interactions: 11 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:T.59, D:R.88, D:T.89, D:S.90, D:S.90, D:R.149, D:R.149, D:S.152, C:F.67, C:K.68 Water bridges: D:R.88, D:R.88 Salt bridges: D:R.149, C:K.68 COA.14: 20 residues within 4Å: Chain E: V.58, T.59, L.60, G.87, R.88, T.89, S.90, V.118, P.125, R.149, S.152 Chain F: V.32, G.34, L.37, L.66, F.67, K.68, E.69, P.70 Ligands: CL.15 12 PLIP interactions: 8 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:T.59, E:R.88, E:R.88, E:T.89, E:S.90, E:S.90, E:R.149, F:F.67, F:K.68 Salt bridges: E:R.149, F:K.68 Water bridges: F:I.71 COA.18: 21 residues within 4Å: Chain E: V.32, G.34, L.37, L.66, F.67, K.68, E.69, P.70 Chain F: V.58, T.59, L.60, G.87, R.88, T.89, S.90, V.118, P.125, R.149, S.152, L.153 Ligands: CL.16 14 PLIP interactions: 11 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:T.59, F:R.88, F:T.89, F:S.90, F:S.90, F:R.149, F:R.149, F:S.152, E:F.67, E:K.68 Water bridges: F:R.88, F:R.88 Salt bridges: F:R.149, E:K.68

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

CL.3: 4 residues within 4Å: Chain A: V.58, T.59 Chain B: G.34 Ligands: COA.2 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: G.34 Chain B: V.58, T.59 Ligands: COA.6 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain C: V.58, T.59 Chain D: G.34 Ligands: COA.8 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain C: G.34 Chain D: V.58, T.59 Ligands: COA.12 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain E: V.58, T.59 Chain F: G.34 Ligands: COA.14 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain E: G.34 Chain F: V.58, T.59 Ligands: COA.18 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khandokar, Y.B. et al., Structural insights into GDP-mediated regulation of a bacterial acyl-CoA thioesterase. J. Biol. Chem. (2017)

Release Date

2016-09-14

Peptides

Acyl-CoA hydrolase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
B

D
D

E
B

F
D

Acyl-CoA hydrolase

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