SMTL ID : 6hxm.1

Structure of the citryl-CoA lyase core module of human ATP citrate lyase in complex with citrate and CoASH in space group C2221

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-tetramer

Ligands

4 x COA: COENZYME A(Non-covalent)

COA.1: 21 residues within 4Å: Chain A: D.102, R.103, F.104, G.105, A.107, K.133, L.138, I.139, M.140, G.141, I.142, G.143, H.144, R.145, K.187, N.189, L.190, N.193, D.195 Chain C: L.252 Ligands: FLC.2 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.103, A:I.139, A:I.139, A:G.141, A:I.142, A:K.187, A:N.189, A:N.193 Water bridges: A:K.133, A:H.144, A:H.144, A:H.144, A:R.145, A:R.145 Salt bridges: A:K.133, A:R.145, A:K.187 Hydrophobic interactions: C:L.252 COA.3: 17 residues within 4Å: Chain B: A.107, K.133, L.138, I.139, M.140, G.141, I.142, G.143, H.144, R.145, K.186, K.187, N.189, L.190, N.193, D.195 Ligands: FLC.4 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:K.133, B:I.139, B:I.139, B:G.141, B:I.142, B:I.142, B:N.189, B:N.193 Water bridges: B:K.186 Salt bridges: B:K.133, B:K.186, B:K.187 COA.5: 21 residues within 4Å: Chain A: L.252 Chain C: D.102, R.103, F.104, G.105, A.107, K.133, L.138, I.139, M.140, G.141, I.142, G.143, H.144, R.145, K.187, N.189, L.190, N.193, D.195 Ligands: FLC.6 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.103, C:I.139, C:I.139, C:G.141, C:I.142, C:K.187, C:N.189, C:N.193 Water bridges: C:K.133, C:H.144, C:H.144, C:H.144, C:R.145, C:R.145 Salt bridges: C:K.133, C:R.145, C:K.187 Hydrophobic interactions: A:L.252 COA.7: 17 residues within 4Å: Chain D: A.107, K.133, L.138, I.139, M.140, G.141, I.142, G.143, H.144, R.145, K.186, K.187, N.189, L.190, N.193, D.195 Ligands: FLC.8 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:K.133, D:I.139, D:I.139, D:G.141, D:I.142, D:I.142, D:N.189, D:N.193 Water bridges: D:K.186 Salt bridges: D:K.133, D:K.186, D:K.187

4 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 15 residues within 4Å: Chain A: H.69, V.73, F.104, G.105, H.144, R.145, V.146, R.155, N.193, V.194, D.195, F.230, R.234 Chain C: R.254 Ligands: COA.1 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.73, A:F.104 Hydrogen bonds: A:H.69, A:G.105, A:H.144, A:R.155, A:R.155 Salt bridges: A:H.69, A:H.69, A:H.144, A:R.155, A:R.234, C:R.254 FLC.4: 11 residues within 4Å: Chain A: E.16 Chain B: H.69, V.73, F.104, G.105, R.155, D.195, F.230, R.234 Chain D: R.254 Ligands: COA.3 8 PLIP interactions: 1 interactions with chain D, 7 interactions with chain B Salt bridges: D:R.254, B:H.69, B:H.69, B:R.234 Hydrogen bonds: B:G.105 Water bridges: B:H.69, B:G.106, B:R.155 FLC.6: 15 residues within 4Å: Chain A: R.254 Chain C: H.69, V.73, F.104, G.105, H.144, R.145, V.146, R.155, N.193, V.194, D.195, F.230, R.234 Ligands: COA.5 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:V.73, C:F.104 Hydrogen bonds: C:H.69, C:G.105, C:H.144, C:R.155, C:R.155 Salt bridges: C:H.69, C:H.69, C:H.144, C:R.155, C:R.234, A:R.254 FLC.8: 11 residues within 4Å: Chain B: R.254 Chain C: E.16 Chain D: H.69, V.73, F.104, G.105, R.155, D.195, F.230, R.234 Ligands: COA.7 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:G.105 Water bridges: D:H.69, D:G.106, D:R.155 Salt bridges: D:H.69, D:H.69, D:R.234, B:R.254

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

ATP-citrate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

ATP-citrate synthase

Related Entries With Identical Sequence