SMTL ID : 8zrv.1

Structure of human ECHS1 in complex with Hexanoyl-CoA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x HXC: HEXANOYL-COENZYME A(Non-covalent)

HXC.1: 31 residues within 4Å: Chain A: K.29, A.30, L.31, A.33, A.69, G.70, A.71, D.72, I.73, K.74, M.76, L.90, W.93, Y.110, F.112, G.113, G.114, E.117, P.136, E.137, I.140, T.142, I.143, P.144, G.145, A.146, R.170 Chain C: K.233, F.236, F.252, K.255 15 PLIP interactions: 10 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:L.31, A:W.93, A:P.136 Hydrogen bonds: A:K.29, A:A.69, A:A.71, A:D.72, A:I.73, A:K.74, C:K.255 Salt bridges: A:K.74, C:K.255, C:K.255 pi-Stacking: C:F.252, C:F.252 HXC.3: 31 residues within 4Å: Chain A: K.233, F.236, F.252, K.255 Chain B: K.29, A.30, L.31, A.33, A.69, G.70, A.71, D.72, I.73, K.74, M.76, L.90, W.93, Y.110, F.112, G.113, G.114, E.117, P.136, E.137, I.140, T.142, I.143, P.144, G.145, A.146, R.170 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.93, B:F.112, A:F.236, A:F.252 Hydrogen bonds: B:A.71, B:A.71, B:D.72, B:I.73, B:G.114, B:P.136 Salt bridges: B:K.74, A:K.255 HXC.4: 31 residues within 4Å: Chain B: K.233, F.236, F.252, K.255 Chain C: K.29, A.30, L.31, A.33, A.69, G.70, A.71, D.72, I.73, K.74, M.76, L.90, W.93, Y.110, F.112, G.113, G.114, E.117, P.136, E.137, I.140, T.142, I.143, P.144, G.145, A.146, R.170 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:L.31, C:W.93, C:Y.110, C:P.136 Hydrogen bonds: C:A.69, C:D.72, C:I.73, C:T.142, B:K.255 Salt bridges: B:K.255, B:K.255 pi-Stacking: B:F.252 HXC.5: 31 residues within 4Å: Chain D: K.29, A.30, L.31, A.33, A.69, G.70, A.71, D.72, I.73, K.74, M.76, L.90, W.93, Y.110, F.112, G.113, G.114, E.117, P.136, E.137, I.140, T.142, I.143, P.144, G.145, A.146, R.170 Chain F: K.233, F.236, F.252, K.255 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: D:W.93, D:F.112 Hydrogen bonds: D:A.71, D:I.73, D:K.74, D:E.137 Salt bridges: D:K.74, F:K.255 pi-Stacking: F:F.252 HXC.7: 30 residues within 4Å: Chain D: K.233, F.236, F.252, K.255 Chain E: K.29, A.30, L.31, A.33, A.69, G.70, A.71, D.72, I.73, K.74, M.76, L.90, W.93, Y.110, F.112, G.113, G.114, E.117, P.136, E.137, I.140, T.142, P.144, G.145, A.146, R.170 12 PLIP interactions: 9 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:A.71, E:L.90, E:P.136, D:F.252 Hydrogen bonds: E:A.69, E:A.71, E:I.73, E:K.74, E:E.137 Salt bridges: E:K.74, D:K.255 pi-Stacking: D:F.252 HXC.8: 30 residues within 4Å: Chain E: K.233, F.236, F.252, K.255 Chain F: K.29, A.30, L.31, A.33, A.69, G.70, A.71, D.72, I.73, K.74, M.76, L.90, W.93, Y.110, F.112, G.113, G.114, E.117, P.136, E.137, I.140, T.142, P.144, G.145, A.146, R.170 9 PLIP interactions: 7 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:W.93, F:W.93, F:P.136, E:F.252 Hydrogen bonds: F:A.69, F:A.71, F:I.73, F:R.170 Salt bridges: E:K.255

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: A.179 Chain B: A.179 Chain C: A.179 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:A.179 MG.6: 3 residues within 4Å: Chain D: A.179 Chain E: A.179 Chain F: A.179 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Metal complexes: D:A.179, E:A.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Su, G. et al., Structural and biochemical mechanism of short-chain enoyl-CoA hydratase (ECHS1) substrate recognition. Commun Biol (2025)

Release Date

2025-04-30

Peptides

Enoyl-CoA hydratase, mitochondrial: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Enoyl-CoA hydratase, mitochondrial

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