SMTL ID : 7wiz.1

Structural basis for ligand binding modes of CTP synthase

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x GLN: GLUTAMINE(Non-covalent)

GLN.1: 12 residues within 4Å: Chain A: G.371, G.372, F.373, C.399, L.400, Q.403, R.479, H.480, R.481, Y.482, Q.524, H.526 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:F.373, A:L.400 Hydrogen bonds: A:G.372, A:Q.403, A:Q.403, A:R.479, A:R.481, A:Y.482 GLN.5: 12 residues within 4Å: Chain B: G.371, G.372, F.373, C.399, L.400, Q.403, R.479, H.480, R.481, Y.482, Q.524, H.526 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:F.373, B:L.400 Hydrogen bonds: B:G.372, B:Q.403, B:Q.403, B:R.479, B:R.481, B:Y.482 GLN.7: 12 residues within 4Å: Chain C: G.371, G.372, F.373, C.399, L.400, Q.403, R.479, H.480, R.481, Y.482, Q.524, H.526 9 PLIP interactions: 7 interactions with chain C, 2 Ligand-Ligand interactions Hydrophobic interactions: C:F.373, C:L.400 Hydrogen bonds: C:G.372, C:Q.403, C:R.479, C:R.481, C:Y.482, Q.7, Q.7 GLN.11: 12 residues within 4Å: Chain D: G.371, G.372, F.373, C.399, L.400, Q.403, R.479, H.480, R.481, Y.482, Q.524, H.526 9 PLIP interactions: 7 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:F.373, D:L.400 Hydrogen bonds: D:G.372, D:Q.403, D:R.479, D:R.481, D:Y.482, Q.11, Q.11

4 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.2: 25 residues within 4Å: Chain A: S.12, G.13, V.14, G.15, K.16, G.17, V.18, K.38, D.70, N.73, E.145, G.147, G.148, R.216, I.243, H.244, D.245, L.246, S.248, I.249, V.252, K.319 Chain B: A.187, T.188 Ligands: UTP.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.13, A:V.14, A:G.15, A:G.15, A:K.16, A:K.16, A:G.17, A:V.18, A:K.38, A:L.246 ACP.6: 25 residues within 4Å: Chain A: A.187, T.188 Chain B: S.12, G.13, V.14, G.15, K.16, G.17, V.18, K.38, D.70, N.73, E.145, G.147, G.148, R.216, I.243, H.244, D.245, L.246, S.248, I.249, V.252, K.319 Ligands: UTP.3 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.13, B:V.14, B:G.15, B:G.15, B:K.16, B:K.16, B:G.17, B:V.18, B:K.38, B:R.216, B:L.246 ACP.8: 25 residues within 4Å: Chain C: S.12, G.13, V.14, G.15, K.16, G.17, V.18, K.38, D.70, N.73, E.145, G.147, G.148, R.216, I.243, H.244, D.245, L.246, S.248, I.249, V.252, K.319 Chain D: A.187, T.188 Ligands: UTP.10 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:S.12, C:G.13, C:V.14, C:G.15, C:G.15, C:K.16, C:K.16, C:G.17, C:V.18, C:K.38, C:R.216, C:L.246 ACP.12: 25 residues within 4Å: Chain C: A.187, T.188 Chain D: S.12, G.13, V.14, G.15, K.16, G.17, V.18, K.38, D.70, N.73, E.145, G.147, G.148, R.216, I.243, H.244, D.245, L.246, S.248, I.249, V.252, K.319 Ligands: UTP.9 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.13, D:V.14, D:G.15, D:G.15, D:K.16, D:K.16, D:G.17, D:V.18, D:K.38, D:R.216, D:L.246

4 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)

UTP.3: 19 residues within 4Å: Chain A: E.190, P.191, K.192, T.193, K.194, Q.197, K.228 Chain B: S.12, K.38, D.40, P.41, Y.42, H.55, G.147, G.148, E.154 Chain D: T.110, Q.112 Ligands: ACP.6 19 PLIP interactions: 9 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:T.193, A:T.193, A:K.194, A:Q.197, B:S.12, B:S.12, B:K.38, B:D.40, B:D.40, B:Y.42, B:H.55, B:E.154, B:E.154 Salt bridges: A:K.192, A:K.194, A:K.194, A:K.228, A:K.228 pi-Stacking: B:H.55 UTP.4: 19 residues within 4Å: Chain A: S.12, K.38, D.40, P.41, Y.42, H.55, G.147, G.148, E.154 Chain B: E.190, P.191, K.192, T.193, K.194, Q.197, K.228 Chain C: T.110, Q.112 Ligands: ACP.2 20 PLIP interactions: 10 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:T.193, B:T.193, B:T.193, B:K.194, B:Q.197, A:S.12, A:S.12, A:K.38, A:D.40, A:D.40, A:Y.42, A:H.55, A:E.154, A:E.154 Salt bridges: B:K.192, B:K.194, B:K.194, B:K.228, B:K.228 pi-Stacking: A:H.55 UTP.9: 19 residues within 4Å: Chain B: T.110, Q.112 Chain C: E.190, P.191, K.192, T.193, K.194, Q.197, K.228 Chain D: S.12, K.38, D.40, P.41, Y.42, H.55, G.147, G.148, E.154 Ligands: ACP.12 16 PLIP interactions: 8 interactions with chain C, 8 interactions with chain D Hydrogen bonds: C:T.193, C:K.194, C:Q.197, D:S.12, D:S.12, D:K.38, D:D.40, D:Y.42, D:H.55, D:E.154 Salt bridges: C:K.192, C:K.194, C:K.194, C:K.228, C:K.228 pi-Stacking: D:H.55 UTP.10: 19 residues within 4Å: Chain A: T.110, Q.112 Chain C: S.12, K.38, D.40, P.41, Y.42, H.55, G.147, G.148, E.154 Chain D: E.190, P.191, K.192, T.193, K.194, Q.197, K.228 Ligands: ACP.8 16 PLIP interactions: 7 interactions with chain C, 9 interactions with chain D Hydrogen bonds: C:S.12, C:K.38, C:D.40, C:Y.42, C:H.55, C:E.154, D:T.193, D:T.193, D:K.194, D:Q.197 pi-Stacking: C:H.55 Salt bridges: D:K.192, D:K.194, D:K.194, D:K.228, D:K.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, X. et al., Structural basis for ligand binding modes of CTP synthase. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2023-01-11

Peptides

CTP synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

CTP synthase

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