SMTL ID : 6hxj.1

Structure of ATP citrate lyase from Chlorobium limicola in complex with citrate and coenzyme A.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.58 Å

Oligo State

hetero-4-4-mer

Ligands

8 x FLC: CITRATE ANION(Non-covalent)

FLC.1: 8 residues within 4Å: Chain A: A.266, S.292, G.293, A.323, N.324, F.325, T.326, R.357 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.325 Hydrogen bonds: A:S.292, A:G.293, A:N.324, A:N.324, A:F.325, A:T.326, A:T.326, A:T.326, A:T.326, A:T.326 Salt bridges: A:R.357 FLC.4: 12 residues within 4Å: Chain B: H.415, V.419, R.449, F.450, G.451, H.491, R.502, V.542, D.543, F.564, R.568 Chain F: R.588 13 PLIP interactions: 1 interactions with chain F, 12 interactions with chain B Salt bridges: F:R.588, B:H.415, B:H.415, B:H.491, B:R.502, B:R.568 Hydrophobic interactions: B:F.450, B:F.564 Hydrogen bonds: B:G.451, B:R.502, B:R.502 Water bridges: B:N.541, B:D.543 FLC.7: 9 residues within 4Å: Chain C: S.292, G.293, A.323, N.324, F.325, T.326, R.357 Chain D: G.178 Ligands: TRS.13 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.325 Hydrogen bonds: C:S.292, C:G.293, C:N.324, C:N.324, C:F.325, C:T.326, C:T.326, C:T.326, C:T.326 Salt bridges: C:R.357 FLC.12: 13 residues within 4Å: Chain D: H.415, V.419, R.449, F.450, G.451, H.491, R.502, N.541, V.542, D.543, F.564, R.568 Chain H: R.588 10 PLIP interactions: 1 interactions with chain H, 9 interactions with chain D Salt bridges: H:R.588, D:H.415, D:H.415, D:H.491, D:R.502, D:R.568 Hydrogen bonds: D:G.451, D:H.491, D:R.502, D:R.502 FLC.16: 8 residues within 4Å: Chain E: S.292, G.293, A.323, N.324, F.325, T.326, R.357 Chain F: G.178 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:F.325 Hydrogen bonds: E:S.292, E:G.293, E:N.324, E:N.324, E:F.325, E:T.326, E:T.326, E:T.326, E:T.326 Salt bridges: E:R.357 FLC.19: 12 residues within 4Å: Chain B: R.588 Chain F: H.415, V.419, R.449, F.450, G.451, H.491, R.502, V.542, D.543, F.564, R.568 10 PLIP interactions: 9 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:F.564 Hydrogen bonds: F:G.451, F:R.502, F:R.502 Salt bridges: F:H.415, F:H.415, F:H.491, F:R.502, F:R.568, B:R.588 FLC.21: 10 residues within 4Å: Chain G: A.266, S.292, G.293, A.323, N.324, F.325, T.326, R.357 Chain H: I.139, G.178 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:G.293, G:N.324, G:N.324, G:F.325, G:T.326, G:T.326, G:T.326 Salt bridges: G:R.357 FLC.24: 12 residues within 4Å: Chain D: R.588 Chain H: H.415, V.419, F.450, G.451, H.491, R.502, N.541, V.542, D.543, F.564, R.568 11 PLIP interactions: 10 interactions with chain H, 1 interactions with chain D Hydrophobic interactions: H:V.419 Hydrogen bonds: H:G.451, H:H.491, H:R.502, H:R.502 Salt bridges: H:H.415, H:H.415, H:H.491, H:R.502, H:R.568, D:R.588

8 x COA: COENZYME A(Non-covalent)

COA.2: 7 residues within 4Å: Chain B: K.480, P.485, V.486, I.489, K.534, K.535, L.538 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.486, B:I.489, B:K.535 Salt bridges: B:K.480, B:K.534, B:K.535 COA.3: 14 residues within 4Å: Chain A: F.325 Chain B: A.18, Y.44, P.45, P.46, Y.85, L.86, G.87, R.90, I.110, T.111, E.112, V.151 Chain H: K.480 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain H Hydrophobic interactions: B:A.18, B:I.110 Hydrogen bonds: B:Y.44, B:L.86, B:G.87, B:R.90, B:R.90, B:E.112, B:E.112 pi-Cation interactions: B:R.90, B:R.90 Salt bridges: H:K.480 COA.10: 8 residues within 4Å: Chain D: K.480, P.485, V.486, I.489, K.534, K.535, L.538 Chain E: K.248 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:V.486, D:I.489 Salt bridges: D:K.480, D:K.534, D:K.535, D:K.535, E:K.248, E:K.248 COA.11: 11 residues within 4Å: Chain D: A.18, Y.44, P.45, P.46, Y.85, L.86, G.87, R.90, I.110, T.111, E.112 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:A.18 Hydrogen bonds: D:Y.44, D:Y.44, D:G.87, D:R.90, D:R.90, D:R.90, D:E.112 pi-Cation interactions: D:R.90, D:R.90 COA.17: 7 residues within 4Å: Chain F: K.480, P.485, V.486, I.489, K.534, K.535, L.538 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:V.486, F:I.489 Salt bridges: F:K.480, F:K.534, F:K.535, F:K.535 COA.18: 11 residues within 4Å: Chain F: A.18, Y.44, P.45, P.46, Y.85, L.86, G.87, R.90, I.110, T.111, E.112 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:A.18 Hydrogen bonds: F:Y.44, F:G.87, F:R.90, F:R.90, F:R.90, F:E.112 Water bridges: F:G.16, F:G.16 pi-Cation interactions: F:R.90, F:R.90 COA.22: 9 residues within 4Å: Chain A: K.248 Chain B: V.17 Chain H: K.480, P.485, V.486, I.489, K.534, K.535, L.538 9 PLIP interactions: 6 interactions with chain H, 3 interactions with chain A Hydrogen bonds: H:V.486, H:I.489 Salt bridges: H:K.480, H:K.534, H:K.535, H:K.535, A:K.248, A:K.248, A:K.248 COA.23: 12 residues within 4Å: Chain G: K.248 Chain H: A.18, Y.44, P.45, P.46, Y.85, L.86, G.87, R.90, I.110, T.111, E.112 10 PLIP interactions: 1 interactions with chain G, 9 interactions with chain H Salt bridges: G:K.248 Hydrophobic interactions: H:A.18 Hydrogen bonds: H:Y.44, H:G.87, H:R.90, H:R.90, H:R.90, H:E.112 pi-Cation interactions: H:R.90, H:R.90

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

PGE.5: 2 residues within 4Å: Chain B: E.215, K.219 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.219 PGE.9: 3 residues within 4Å: Chain C: A.2, Q.185, Y.212 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.2, C:Q.185, C:Q.185 PGE.15: 4 residues within 4Å: Chain D: R.294, G.297, Y.299, K.313 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.294, D:K.313 PGE.20: 4 residues within 4Å: Chain D: G.49 Chain F: K.599 Chain H: K.394, K.395 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.599 Water bridges: F:K.599 PGE.25: 7 residues within 4Å: Chain H: K.462, E.466, P.519, C.520, M.551, D.552, D.554 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:K.462, H:E.466

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.6: 6 residues within 4Å: Chain B: E.53 Chain D: Y.590 Chain F: E.352, P.353, L.354, R.356 6 PLIP interactions: 4 interactions with chain D, 1 interactions with chain F, 1 interactions with chain B Hydrogen bonds: D:Y.590, F:E.352, B:E.53 Water bridges: D:S.584, D:S.584, D:R.585 TRS.13: 7 residues within 4Å: Chain C: G.267, G.268, G.269 Chain D: S.176, G.177, G.178 Ligands: FLC.7 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:G.268, C:G.269, D:G.177, D:G.178

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

PG4.8: 5 residues within 4Å: Chain C: D.102, A.103, K.122, I.164, K.196 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.196 Water bridges: C:K.196 PG4.14: 6 residues within 4Å: Chain B: N.393, K.394, K.395 Chain D: K.599 Chain F: G.49, T.64 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 1 interactions with chain F Hydrogen bonds: B:K.395, D:K.599 Water bridges: F:Q.51

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 lyase beta-subunit: ACEG
ATP-citrate lyase alpha-subunit: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

B
B

D
D

F
F

H
H

ATP-citrate lyase beta-subunit

ATP-citrate lyase alpha-subunit