SMTL ID : 6hxp.1

Structure of citryl-CoA lyase from Hydrogenobacter thermophilus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-tetramer

Ligands

4 x COA: COENZYME A(Non-covalent)

COA.1: 19 residues within 4Å: Chain A: S.97, A.98, A.102, D.105, L.128, K.132, P.133, I.134, P.135, G.136, Y.137, G.138, H.139, R.140, K.143, K.180, K.182, L.184, N.187 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:I.134, A:I.134, A:G.136, A:G.138, A:G.138, A:R.140 Salt bridges: A:K.143, A:K.143, A:K.180, A:K.182 COA.4: 19 residues within 4Å: Chain B: S.97, A.98, A.102, D.105, L.128, K.132, P.133, I.134, P.135, G.136, Y.137, G.138, H.139, R.140, K.143, K.180, K.182, L.184, N.187 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:I.134, B:I.134, B:G.136, B:G.138, B:G.138 Water bridges: B:N.187 Salt bridges: B:K.143, B:K.143, B:K.180, B:K.182 COA.7: 19 residues within 4Å: Chain C: S.97, A.98, A.102, D.105, L.128, K.132, P.133, I.134, P.135, G.136, Y.137, G.138, H.139, R.140, K.143, K.180, K.182, L.184, N.187 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:I.134, C:I.134, C:G.136, C:G.138, C:G.138, C:R.140 Salt bridges: C:K.143, C:K.143, C:K.180, C:K.182 COA.10: 19 residues within 4Å: Chain D: S.97, A.98, A.102, D.105, L.128, K.132, P.133, I.134, P.135, G.136, Y.137, G.138, H.139, R.140, K.143, K.180, K.182, L.184, N.187 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:I.134, D:I.134, D:G.136, D:G.138, D:G.138 Water bridges: D:N.187 Salt bridges: D:K.143, D:K.143, D:K.180, D:K.182

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 7 residues within 4Å: Chain A: Q.35, L.45, P.46, T.47, E.48, S.51 Chain C: L.256 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.35, A:S.51 Water bridges: A:Q.35 SO4.3: 6 residues within 4Å: Chain A: G.29, N.30, L.31, S.32 Chain D: R.52, E.55 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:G.29 Water bridges: D:E.55 SO4.5: 7 residues within 4Å: Chain B: Q.35, L.45, P.46, T.47, E.48, S.51 Chain D: L.256 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.35 Water bridges: B:Q.35 SO4.6: 6 residues within 4Å: Chain B: G.29, N.30, L.31, S.32 Chain C: R.52, E.55 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Water bridges: C:E.55, C:E.55 Hydrogen bonds: B:G.29 SO4.8: 7 residues within 4Å: Chain A: L.256 Chain C: Q.35, L.45, P.46, T.47, E.48, S.51 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.35, C:S.51 Water bridges: C:Q.35 SO4.9: 6 residues within 4Å: Chain B: R.52, E.55 Chain C: G.29, N.30, L.31, S.32 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Water bridges: B:E.55 Hydrogen bonds: C:G.29 SO4.11: 7 residues within 4Å: Chain B: L.256 Chain D: Q.35, L.45, P.46, T.47, E.48, S.51 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.35 Water bridges: D:Q.35 SO4.12: 6 residues within 4Å: Chain A: R.52, E.55 Chain D: G.29, N.30, L.31, S.32 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Water bridges: A:E.55, A:E.55 Hydrogen bonds: D:G.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Verschueren, K.H.G. et al., Structure of ATP citrate lyase and the origin of citrate synthase in the Krebs cycle. Nature (2019)

Release Date

2019-04-10

Peptides

Citryl-CoA lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Citryl-CoA lyase