SMTL ID : 5v3a.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 COA: COENZYME A(Non-covalent)

COA.1: 21 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, L.153 Chain B: V.32, H.33, G.34, L.37, L.66, F.67, K.68, E.69, P.70 18 PLIP interactions: 12 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:V.118, A:P.125 Hydrogen bonds: A:T.59, A:R.88, A:T.89, A:S.90, A:S.90, A:R.149, A:R.149, A:S.152, B:F.67, B:K.68 Water bridges: A:T.89, B:S.29, B:G.34 Salt bridges: A:R.149, B:K.68, B:K.68 COA.3: 20 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 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:V.118 Hydrogen bonds: B:T.59, B:R.88, B:T.89, B:S.90, B:R.149, B:R.149, B:S.152, A:F.67, A:K.68 Water bridges: B:T.59, B:R.88, B:T.89, B:S.152, A:S.29 Salt bridges: B:R.149, A:K.68 COA.5: 21 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, L.153 Chain D: V.32, H.33, G.34, L.37, L.66, F.67, K.68, E.69, P.70 18 PLIP interactions: 12 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:V.118, C:P.125 Hydrogen bonds: C:T.59, C:R.88, C:T.89, C:S.90, C:S.90, C:R.149, C:R.149, C:S.152, D:F.67, D:K.68 Water bridges: C:T.89, D:S.29, D:G.34 Salt bridges: C:R.149, D:K.68, D:K.68 COA.7: 20 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 17 PLIP interactions: 4 interactions with chain C, 13 interactions with chain D Hydrogen bonds: C:F.67, C:K.68, D:T.59, D:R.88, D:T.89, D:S.90, D:R.149, D:R.149, D:S.152 Water bridges: C:S.29, D:T.59, D:R.88, D:T.89, D:S.152 Salt bridges: C:K.68, D:R.149 Hydrophobic interactions: D:V.118 COA.9: 21 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, L.153 Chain F: V.32, H.33, G.34, L.37, L.66, F.67, K.68, E.69, P.70 18 PLIP interactions: 12 interactions with chain E, 6 interactions with chain F Hydrophobic interactions: E:V.118, E:P.125 Hydrogen bonds: E:T.59, E:R.88, E:T.89, E:S.90, E:S.90, E:R.149, E:R.149, E:S.152, F:F.67, F:K.68 Water bridges: E:T.89, F:S.29, F:G.34 Salt bridges: E:R.149, F:K.68, F:K.68 COA.11: 20 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 17 PLIP interactions: 4 interactions with chain E, 13 interactions with chain F Hydrogen bonds: E:F.67, E:K.68, F:T.59, F:R.88, F:T.89, F:S.90, F:R.149, F:R.149, F:S.152 Water bridges: E:S.29, F:T.59, F:R.88, F:T.89, F:S.152 Salt bridges: E:K.68, F:R.149 Hydrophobic interactions: F:V.118

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

GDP.2: 18 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, K.144 Chain B: D.158, M.159, S.160, C.161 Chain D: R.8 21 PLIP interactions: 19 interactions with chain A, 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: A:A.81, A:A.81, A:A.82, A:N.84, A:N.84, A:G.94, A:S.112, A:R.141, D:R.8, B:C.161 Water bridges: A:S.112, A:Y.114, A:Y.114, A:Y.114 Salt bridges: A:E.14, A:R.96, A:H.109, A:R.141, A:R.141, A:K.144 pi-Cation interactions: A:R.141 GDP.4: 18 residues within 4Å: Chain A: D.158, M.159, S.160, C.161 Chain B: E.14, L.15, Y.80, A.81, A.82, N.84, G.94, I.95, R.96, H.109, S.112, Y.114, R.141 Chain E: R.8 18 PLIP interactions: 15 interactions with chain B, 1 interactions with chain E, 2 interactions with chain A Hydrogen bonds: B:L.15, B:A.81, B:A.81, B:A.82, B:N.84, B:N.84, B:G.94, B:S.112, B:Y.114, E:R.8, A:S.160 Water bridges: B:R.96, B:Y.114, A:D.158 Salt bridges: B:E.14, B:R.96, B:H.109, B:R.141 GDP.6: 18 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, K.144 Chain D: D.158, M.159, S.160, C.161 Chain F: R.8 20 PLIP interactions: 18 interactions with chain C, 1 interactions with chain D, 1 interactions with chain F Hydrogen bonds: C:A.81, C:A.81, C:A.82, C:N.84, C:N.84, C:G.94, C:S.112, C:Y.114, C:R.141, D:C.161, F:R.8 Water bridges: C:S.112, C:Y.114 Salt bridges: C:E.14, C:R.96, C:H.109, C:R.141, C:R.141, C:K.144 pi-Cation interactions: C:R.141 GDP.8: 18 residues within 4Å: Chain A: R.8 Chain C: D.158, M.159, S.160, C.161 Chain D: E.14, L.15, Y.80, A.81, A.82, N.84, G.94, I.95, R.96, H.109, S.112, Y.114, R.141 17 PLIP interactions: 2 interactions with chain C, 14 interactions with chain D, 1 interactions with chain A Hydrogen bonds: C:S.160, D:L.15, D:A.81, D:A.81, D:A.82, D:N.84, D:N.84, D:G.94, D:S.112, A:R.8 Water bridges: C:D.158, D:R.96, D:Y.114 Salt bridges: D:E.14, D:R.96, D:H.109, D:R.141 GDP.10: 18 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, K.144 Chain F: D.158, M.159, S.160, C.161 22 PLIP interactions: 2 interactions with chain F, 19 interactions with chain E, 1 interactions with chain B Hydrogen bonds: F:C.161, E:A.81, E:A.81, E:A.82, E:N.84, E:N.84, E:G.94, E:S.112, E:R.141, B:R.8 Water bridges: F:D.158, E:S.112, E:Y.114, E:Y.114, E:Y.114 Salt bridges: E:E.14, E:R.96, E:H.109, E:R.141, E:R.141, E:K.144 pi-Cation interactions: E:R.141 GDP.12: 18 residues within 4Å: Chain C: R.8 Chain E: D.158, M.159, S.160, C.161 Chain F: E.14, L.15, Y.80, A.81, A.82, N.84, G.94, I.95, R.96, H.109, S.112, Y.114, R.141 18 PLIP interactions: 15 interactions with chain F, 2 interactions with chain E, 1 interactions with chain C Hydrogen bonds: F:L.15, F:A.81, F:A.81, F:A.82, F:N.84, F:N.84, F:G.94, F:S.112, F:Y.114, E:S.160, C:R.8 Water bridges: F:R.96, F:Y.114, E:D.158 Salt bridges: F:E.14, F:R.96, F:H.109, F:R.141

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

2017-05-24

Peptides

Acyl-CoA hydrolase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
C

D
D

E
C

F
D

Acyl-CoA hydrolase

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