SMTL ID : 6z2h.1

Citryl-CoA lyase module of human ATP citrate lyase in complex with (3S)-citryl-CoA.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

3 x Q5B: (3S)-citryl-Coenzyme A(Non-covalent)

Q5B.1: 28 residues within 4Å: Chain A: H.69, V.73, D.102, R.103, F.104, G.105, A.107, L.138, I.139, M.140, G.141, I.142, G.143, H.144, R.145, R.155, K.187, N.189, L.190, N.193, V.194, D.195, F.230, R.234 Chain D: L.252, R.254 Ligands: OAA.2, ACO.3 28 PLIP interactions: 26 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:A.107, D:L.252 Hydrogen bonds: A:H.69, A:R.103, A:G.105, A:I.139, A:I.139, A:G.141, A:I.142, A:I.142, A:H.144, A:H.144, A:R.155, A:R.155, A:N.189, A:N.193 Water bridges: A:R.145, A:R.145, A:V.194 Salt bridges: A:H.69, A:H.69, A:H.144, A:R.145, A:R.155, A:K.187, A:K.187, A:R.234, D:R.254 Q5B.4: 26 residues within 4Å: Chain B: L.252, R.254 Chain C: H.69, V.73, D.102, R.103, F.104, G.105, A.107, L.138, I.139, M.140, G.141, I.142, G.143, H.144, R.145, R.155, N.189, L.190, N.193, D.195, F.230, R.234 Ligands: OAA.5, ACO.6 20 PLIP interactions: 18 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:R.103, C:G.105, C:I.139, C:I.139, C:G.141, C:I.142, C:I.142, C:H.144, C:H.144, C:R.155, C:N.189, C:N.193 Salt bridges: C:H.69, C:H.69, C:H.144, C:R.145, C:R.155, C:R.234, B:R.254 Hydrophobic interactions: B:L.252 Q5B.7: 20 residues within 4Å: Chain A: R.254 Chain D: H.69, V.73, A.107, K.133, L.138, I.139, M.140, G.141, I.142, G.143, H.144, R.145, R.155, N.189, L.190, N.193, V.194, D.195, R.234 20 PLIP interactions: 17 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:K.133, D:I.139, D:I.139, D:G.141, D:I.142, D:I.142, D:H.144, D:N.189, D:N.193 Water bridges: D:D.195, D:R.234, A:R.254, A:R.254 Salt bridges: D:H.69, D:H.69, D:K.133, D:H.144, D:R.145, D:R.155, A:R.254

2 x OAA: OXALOACETATE ION(Non-covalent)

OAA.2: 12 residues within 4Å: Chain A: H.69, V.73, F.104, H.144, R.145, R.155, V.194, F.230, R.234 Chain D: R.254 Ligands: Q5B.1, ACO.3 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:V.73 Hydrogen bonds: A:H.69, 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, D:R.254 OAA.5: 11 residues within 4Å: Chain B: R.254 Chain C: H.69, V.73, F.104, H.144, R.145, R.155, F.230, R.234 Ligands: Q5B.4, ACO.6 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.73 Hydrogen bonds: C:H.69, C:H.144, C:R.155, C:R.155 Water bridges: C:H.144 Salt bridges: C:H.69, C:H.69, C:H.144, C:R.155, C:R.234, B:R.254

2 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.3: 23 residues within 4Å: Chain A: D.102, R.103, F.104, G.105, A.107, L.138, I.139, M.140, G.141, I.142, G.143, H.144, R.145, K.187, N.189, L.190, N.193, V.194, D.195, F.230 Chain D: L.252 Ligands: Q5B.1, OAA.2 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:V.194, A:F.230, D:L.252 Hydrogen bonds: A:R.103, A:G.105, A:I.139, A:I.139, A:G.141, A:I.142, A:I.142, A:N.189, A:N.193 Water bridges: A:R.145 Salt bridges: A:R.145, A:K.187 ACO.6: 21 residues within 4Å: Chain B: L.252 Chain C: D.102, R.103, F.104, G.105, A.107, L.138, I.139, M.140, G.141, I.142, G.143, H.144, R.145, N.189, L.190, N.193, D.195, F.230 Ligands: Q5B.4, OAA.5 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.230, B:L.252 Hydrogen bonds: C:R.103, C:G.105, C:I.139, C:I.139, C:G.141, C:I.142, C:I.142, C:N.189, C:N.193 Salt bridges: C:R.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Verstraete, K. et al., Acetyl-CoA is produced by the citrate synthase homology module of ATP-citrate lyase. Nat.Struct.Mol.Biol. (2021)

Release Date

2021-05-26

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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