SMTL ID : 6hxi.1

Structure of ATP citrate lyase from Methanothrix soehngenii in complex with citrate and coenzyme A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-4-4-mer

Ligands

4 x FLC: CITRATE ANION(Non-covalent)

FLC.1: 12 residues within 4Å: Chain A: A.278, S.306, G.307, A.343, N.344, F.345, T.346, R.377 Chain D: S.178, G.179, G.180 Ligands: COA.11 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:S.306, A:S.306, A:G.307, A:N.344, A:N.344, A:F.345, A:T.346, A:T.346, A:T.346, A:T.346, A:T.346, D:G.179, D:G.180 Water bridges: A:G.280, A:G.280, D:S.178 Salt bridges: A:R.377 FLC.9: 11 residues within 4Å: Chain B: G.179, G.180 Chain C: A.278, S.306, G.307, A.343, N.344, F.345, T.346, R.377 Ligands: COA.3 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:S.306, C:G.307, C:N.344, C:N.344, C:F.345, C:T.346, C:T.346, C:T.346, B:G.179, B:G.180 Water bridges: C:G.280, C:G.280, C:G.280, C:G.280, B:S.178 Salt bridges: C:R.377 FLC.14: 12 residues within 4Å: Chain E: A.278, S.306, G.307, A.343, N.344, F.345, T.346, R.377 Chain H: S.178, G.179, G.180 Ligands: COA.24 17 PLIP interactions: 3 interactions with chain H, 14 interactions with chain E Hydrogen bonds: H:G.179, H:G.180, E:S.306, E:S.306, E:G.307, E:N.344, E:N.344, E:F.345, E:T.346, E:T.346, E:T.346, E:T.346, E:T.346 Water bridges: H:S.178, E:G.280, E:G.280 Salt bridges: E:R.377 FLC.22: 11 residues within 4Å: Chain F: G.179, G.180 Chain G: A.278, S.306, G.307, A.343, N.344, F.345, T.346, R.377 Ligands: COA.16 16 PLIP interactions: 13 interactions with chain G, 3 interactions with chain F Hydrogen bonds: G:S.306, G:G.307, G:N.344, G:N.344, G:F.345, G:T.346, G:T.346, G:T.346, F:G.179, F:G.180 Water bridges: G:G.280, G:G.280, G:G.280, G:G.280, F:S.178 Salt bridges: G:R.377

4 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: D.255, T.258, A.260 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.255 NA.10: 3 residues within 4Å: Chain C: D.255, T.258, A.260 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.258 NA.15: 3 residues within 4Å: Chain E: D.255, T.258, A.260 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:A.260 NA.23: 3 residues within 4Å: Chain G: D.255, T.258, A.260 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:D.255

4 x COA: COENZYME A(Non-covalent)

COA.3: 23 residues within 4Å: Chain B: Q.21, F.87, A.88, S.89, R.91, S.92, I.112, E.114, A.139, T.140, V.141, G.179 Chain C: G.259, G.307, F.345 Chain F: K.479, N.484, I.485, I.488, K.532, K.533, L.536 Ligands: FLC.9 21 PLIP interactions: 12 interactions with chain B, 6 interactions with chain F, 3 interactions with chain C Hydrophobic interactions: B:E.114 Hydrogen bonds: B:S.89, B:S.89, B:S.92, B:I.112, F:I.485, F:I.485, C:G.259 Water bridges: B:Q.21, B:Q.21, B:S.89, B:R.91, B:S.92, B:E.114, C:G.259, C:G.259 Salt bridges: B:R.91, F:K.479, F:K.532, F:K.533, F:K.533 COA.11: 24 residues within 4Å: Chain A: G.259, G.307, F.345 Chain D: Q.21, F.87, A.88, S.89, R.91, S.92, I.112, E.114, A.139, T.140, V.141, G.179 Chain H: K.479, N.484, I.485, I.488, T.529, K.532, K.533, L.536 Ligands: FLC.1 18 PLIP interactions: 6 interactions with chain H, 11 interactions with chain D, 1 interactions with chain A Hydrogen bonds: H:I.485, H:I.485, D:S.89, D:S.89, D:S.92, D:I.112, A:G.259 Salt bridges: H:K.479, H:K.532, H:K.533, H:K.533, D:R.91 Hydrophobic interactions: D:E.114 Water bridges: D:Q.21, D:Q.21, D:S.89, D:S.92, D:E.114 COA.16: 23 residues within 4Å: Chain B: K.479, N.484, I.485, I.488, K.532, K.533, L.536 Chain F: Q.21, F.87, A.88, S.89, R.91, S.92, I.112, E.114, A.139, T.140, V.141, G.179 Chain G: G.259, G.307, F.345 Ligands: FLC.22 21 PLIP interactions: 12 interactions with chain F, 6 interactions with chain B, 3 interactions with chain G Hydrophobic interactions: F:E.114 Hydrogen bonds: F:S.89, F:S.89, F:S.92, F:I.112, B:I.485, B:I.485, G:G.259 Water bridges: F:Q.21, F:Q.21, F:S.89, F:R.91, F:S.92, F:E.114, G:G.259, G:G.259 Salt bridges: F:R.91, B:K.479, B:K.532, B:K.533, B:K.533 COA.24: 24 residues within 4Å: Chain D: K.479, N.484, I.485, I.488, T.529, K.532, K.533, L.536 Chain E: G.259, G.307, F.345 Chain H: Q.21, F.87, A.88, S.89, R.91, S.92, I.112, E.114, A.139, T.140, V.141, G.179 Ligands: FLC.14 18 PLIP interactions: 11 interactions with chain H, 6 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: H:E.114 Hydrogen bonds: H:S.89, H:S.89, H:S.92, H:I.112, D:I.485, D:I.485, E:G.259 Water bridges: H:Q.21, H:Q.21, H:S.89, H:S.92, H:E.114 Salt bridges: H:R.91, D:K.479, D:K.532, D:K.533, D:K.533

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 7 residues within 4Å: Chain B: G.52, I.53, M.67, Y.68 Chain H: R.593, L.594, G.595 No protein-ligand interaction detected (PLIP) PGE.5: 6 residues within 4Å: Chain B: M.609, P.611, E.615 Chain F: I.53 Chain H: T.358, K.394 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain H Water bridges: B:E.615, H:K.394, H:K.394 PGE.17: 7 residues within 4Å: Chain D: R.593, L.594, G.595 Chain F: G.52, I.53, M.67, Y.68 No protein-ligand interaction detected (PLIP) PGE.18: 6 residues within 4Å: Chain B: I.53 Chain D: T.358, K.394 Chain F: M.609, P.611, E.615 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain D Water bridges: F:E.615, D:K.394, D:K.394

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 8 residues within 4Å: Chain B: K.592, R.593, G.595 Chain F: E.565 Chain H: G.52, I.53, M.67, Y.68 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:E.565, F:E.565 PG4.19: 8 residues within 4Å: Chain B: E.565 Chain D: G.52, I.53, M.67, Y.68 Chain F: K.592, R.593, G.595 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.565, B:E.565

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 3 residues within 4Å: Chain B: G.298, A.299, Y.300 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.300 Hydrogen bonds: B:Y.300 ACT.8: 6 residues within 4Å: Chain B: H.415, V.419, F.450, R.501, F.576, R.580 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.576 Salt bridges: B:H.415, B:R.501, B:R.580 ACT.13: 5 residues within 4Å: Chain D: H.415, R.501, D.541, F.576, R.580 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.576 Hydrogen bonds: D:D.541 Water bridges: D:R.501 Salt bridges: D:H.415, D:R.501, D:R.580 ACT.20: 3 residues within 4Å: Chain F: G.298, A.299, Y.300 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:Y.300 Hydrogen bonds: F:Y.300 ACT.21: 6 residues within 4Å: Chain F: H.415, V.419, F.450, R.501, F.576, R.580 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:F.576 Salt bridges: F:H.415, F:R.501, F:R.580 ACT.26: 5 residues within 4Å: Chain H: H.415, R.501, D.541, F.576, R.580 6 PLIP interactions: 6 interactions with chain H Hydrophobic interactions: H:F.576 Hydrogen bonds: H:D.541 Water bridges: H:R.501 Salt bridges: H:H.415, H:R.501, H:R.580

2 x SIN: SUCCINIC ACID(Non-covalent)

SIN.12: 7 residues within 4Å: Chain D: R.593 Chain H: W.392, F.393, K.394, K.395, F.558, Y.571 7 PLIP interactions: 5 interactions with chain H, 2 interactions with chain D Water bridges: H:T.358, H:K.394, H:Y.571 Salt bridges: H:K.394, H:K.395, D:R.593, D:R.593 SIN.25: 7 residues within 4Å: Chain D: W.392, F.393, K.394, K.395, F.558, Y.571 Chain H: R.593 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain H Water bridges: D:T.358, D:K.394, D:Y.571 Salt bridges: D:K.394, D:K.395, H:R.593, H:R.593

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

Citrate lyase, subunit 1: ACEG
Succinyl-CoA ligase (ADP-forming) subunit alpha: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
A

G
C

B
B

D
D

F
B

H
D

Citrate lyase, subunit 1

Succinyl-CoA ligase (ADP-forming) subunit alpha

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