SMTL ID : 8zry.1

Structure of human ECHS1 in complex with Crotonoyl-CoA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x 01: S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (E)-but-2-enethioate

01.1: 28 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, P.144, G.145, A.146, R.170 Chain C: F.252, K.255 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:L.31, A:L.90, A:F.112, A:F.112, A:P.136, A:E.137, A:A.146 Hydrogen bonds: A:A.69, A:A.71, A:A.71, A:D.72, A:I.73, A:K.74, A:G.114 Salt bridges: A:K.74, C:K.255 pi-Stacking: C:F.252, C:F.252 01.3: 27 residues within 4Å: Chain A: 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, 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 18 PLIP interactions: 13 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.31, B:L.90, B:W.93, B:F.112, B:F.112, B:P.136 Hydrogen bonds: B:A.71, B:A.71, B:D.72, B:I.73, B:G.114, B:P.136, A:K.255 Salt bridges: B:K.74, A:K.255, A:K.255 pi-Stacking: A:F.252, A:F.252 01.4: 25 residues within 4Å: Chain B: F.252, K.255 Chain C: K.29, A.30, L.31, A.33, A.69, G.70, A.71, D.72, I.73, L.90, W.93, Y.110, F.112, G.113, G.114, E.117, P.136, E.137, I.140, P.144, G.145, A.146, R.170 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.31, C:A.71, C:L.90, C:W.93, C:F.112, C:F.112, B:F.252 Hydrogen bonds: C:A.71, C:A.71, C:D.72, C:I.73, C:G.114 Salt bridges: B:K.255, B:K.255 01.5: 27 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, 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 Chain F: F.252, K.255 17 PLIP interactions: 13 interactions with chain D, 4 interactions with chain F Hydrophobic interactions: D:L.31, D:A.71, D:L.90, D:Y.110, D:F.112, D:F.112 Hydrogen bonds: D:A.69, D:A.71, D:A.71, D:I.73, D:G.114, D:E.137, F:K.255 Salt bridges: D:K.74, F:K.255, F:K.255 pi-Stacking: F:F.252 01.7: 27 residues within 4Å: Chain D: 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, 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 17 PLIP interactions: 15 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:L.31, E:L.90, E:Y.110, E:F.112, E:F.112, E:P.136, E:A.146, D:F.252 Hydrogen bonds: E:A.69, E:A.71, E:A.71, E:I.73, E:K.74, E:G.114, E:E.137 Salt bridges: E:K.74, D:K.255 01.8: 28 residues within 4Å: Chain E: 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 17 PLIP interactions: 13 interactions with chain F, 4 interactions with chain E Hydrophobic interactions: F:L.31, F:L.90, F:F.112, F:F.112, F:P.136, F:A.146 Hydrogen bonds: F:A.69, F:A.71, F:A.71, F:I.73, F:G.114, F:E.137 Salt bridges: F:K.74, E:K.255, E:K.255 pi-Stacking: E:F.252, E:F.252

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 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain D: A.179 Chain E: A.179 Chain F: A.179 No protein-ligand interaction detected (PLIP)

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

Related Entries With Identical Sequence