SMTL ID : 6hxl.1 (1 other biounit)

Structure of the citryl-CoA lyase core module of human ATP citrate lyase in complex with citrate and CoASH (space group P21)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 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 B: L.252 Ligands: FLC.2 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.103, A:I.139, A:I.139, A:G.141, A:I.142, A:I.142, A:I.142, A:N.189, A:N.193 Water bridges: A:H.144, A:H.144, A:R.145, A:R.145, A:R.145 Salt bridges: A:K.133, A:R.145, A:K.187 Hydrophobic interactions: B:L.252 COA.3: 21 residues within 4Å: Chain A: L.252 Chain B: 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.4 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.103, B:I.139, B:I.139, B:G.141, B:I.142, B:I.142, B:N.189, B:N.193 Water bridges: B:H.144, B:H.144, B:H.144, B:R.145, B:R.145 Salt bridges: B:K.133, B:R.145, B:K.187 Hydrophobic interactions: A:L.252 COA.6: 21 residues within 4Å: 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 Chain D: L.252 Ligands: FLC.7 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.103, C:K.133, C:I.139, C:I.139, C:G.141, C:I.142, C:I.142, C:N.189, C:N.193 Water bridges: C:R.145, C:R.145 Salt bridges: C:K.133, C:R.145, C:K.187 Hydrophobic interactions: D:L.252 COA.8: 17 residues within 4Å: Chain D: D.102, R.103, A.107, A.110, 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 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:I.139, D:I.139, D:G.141, D:I.142, D:K.186, D:N.189 Water bridges: D:K.187, D:K.187, D:N.193 Salt bridges: D:K.186, D:K.187, D:K.187

3 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 B: R.254 Ligands: COA.1 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.73, A:F.104 Hydrogen bonds: A:G.105, A:H.144, A:R.155, A:R.155 Water bridges: A:H.144 Salt bridges: A:H.69, A:H.69, A:H.144, A:R.155, A:R.234, B:R.254 FLC.4: 15 residues within 4Å: Chain A: R.254 Chain B: 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.3 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.73, B:F.104 Hydrogen bonds: B:H.69, B:G.105, B:H.144, B:R.155, B:R.155 Water bridges: B:H.144 Salt bridges: B:H.69, B:H.69, B:H.144, B:R.155, B:R.234, A:R.254 FLC.7: 15 residues within 4Å: 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 Chain D: R.254 Ligands: COA.6 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain D 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, D:R.254

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 9 residues within 4Å: Chain B: Q.57, E.60, M.61, M.64, Y.162 Chain C: F.32, E.35, G.37, I.38 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain C Water bridges: B:Q.57, B:Q.57, B:Q.57, B:E.60, B:Y.162, C:E.35, C:M.36, C:I.38

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

SO4.9: 7 residues within 4Å: Chain D: H.69, V.73, F.104, G.105, R.155, F.230, R.234 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.234 Salt bridges: D:H.69, D:R.234 SO4.10: 4 residues within 4Å: Chain D: G.18, Q.19, E.20, I.22 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.19, D:E.20 Water bridges: D:G.18, D:E.20, D:E.20

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
C

D
D

ATP-citrate synthase

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