SMTL ID : 8fva.1

E coli. CTP synthase in complex with F-araCTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

2 x MLA: MALONIC ACID(Non-covalent)

MLA.1: 8 residues within 4Å: Chain A: S.14, S.15, L.16, G.17, K.18, K.40, G.142, G.143 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.15, A:L.16, A:G.17, A:K.18, A:G.143, A:G.143 Water bridges: A:V.13, A:K.18, A:G.19 Salt bridges: A:K.18, A:K.18, A:K.40 MLA.6: 8 residues within 4Å: Chain C: S.14, S.15, L.16, G.17, K.18, K.40, G.142, G.143 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:S.15, C:L.16, C:G.17, C:K.18, C:G.143, C:G.143 Water bridges: C:V.13, C:K.18, C:G.19 Salt bridges: C:K.18, C:K.18, C:K.40

4 x 1TK: 4-amino-1-{2-deoxy-2-fluoro-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one(Non-covalent)

1TK.2: 14 residues within 4Å: Chain A: V.186, K.187, T.188, K.189, Q.192, K.223, F.227 Chain B: S.14, D.147, I.148, E.149 Chain D: Q.114, I.116 Ligands: NA.3 27 PLIP interactions: 8 interactions with chain B, 17 interactions with chain A, 2 interactions with chain D Hydrogen bonds: B:S.14, B:S.14, B:T.144, B:I.148, B:E.149, A:T.188, A:T.188, A:K.189, A:K.189, A:Q.192, D:Q.114 Water bridges: B:D.147, B:D.147, B:E.149, A:K.187, A:K.187, A:K.189, A:Q.192 Hydrophobic interactions: A:F.227, D:I.116 Salt bridges: A:K.187, A:K.187, A:K.189, A:K.189, A:K.189, A:K.223, A:K.223 1TK.4: 14 residues within 4Å: Chain A: S.14, D.147, I.148, E.149 Chain B: V.186, K.187, T.188, K.189, Q.192, K.223, F.227 Chain C: Q.114, I.116 Ligands: NA.5 20 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C, 13 interactions with chain B Hydrogen bonds: A:S.14, A:S.14, A:I.148, A:E.149, C:Q.114, B:T.188, B:K.189, B:K.189, B:Q.192 Water bridges: A:E.149, B:K.187, B:K.187 Hydrophobic interactions: C:I.116, B:F.227 Salt bridges: B:K.187, B:K.189, B:K.189, B:K.189, B:K.223, B:K.223 1TK.7: 14 residues within 4Å: Chain B: Q.114, I.116 Chain C: V.186, K.187, T.188, K.189, Q.192, K.223, F.227 Chain D: S.14, D.147, I.148, E.149 Ligands: NA.8 27 PLIP interactions: 8 interactions with chain D, 17 interactions with chain C, 2 interactions with chain B Hydrogen bonds: D:S.14, D:S.14, D:T.144, D:I.148, D:E.149, C:T.188, C:T.188, C:K.189, C:K.189, C:Q.192, B:Q.114 Water bridges: D:D.147, D:D.147, D:E.149, C:K.187, C:K.187, C:K.189, C:Q.192 Hydrophobic interactions: C:F.227, B:I.116 Salt bridges: C:K.187, C:K.187, C:K.189, C:K.189, C:K.189, C:K.223, C:K.223 1TK.9: 14 residues within 4Å: Chain A: Q.114, I.116 Chain C: S.14, D.147, I.148, E.149 Chain D: V.186, K.187, T.188, K.189, Q.192, K.223, F.227 Ligands: NA.10 20 PLIP interactions: 2 interactions with chain A, 5 interactions with chain C, 13 interactions with chain D Hydrophobic interactions: A:I.116, D:F.227 Hydrogen bonds: A:Q.114, C:S.14, C:S.14, C:I.148, C:E.149, D:T.188, D:K.189, D:K.189, D:Q.192 Water bridges: C:E.149, D:K.187, D:K.187 Salt bridges: D:K.187, D:K.189, D:K.189, D:K.189, D:K.223, D:K.223

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

NA.3: 2 residues within 4Å: Chain A: K.223 Ligands: 1TK.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.223, A:K.223 NA.5: 3 residues within 4Å: Chain B: E.185, K.187 Ligands: 1TK.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.185 NA.8: 2 residues within 4Å: Chain C: K.223 Ligands: 1TK.7 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.223 Water bridges: C:K.223 NA.10: 3 residues within 4Å: Chain D: E.185, K.187 Ligands: 1TK.9 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McLeod, M.J. et al., A metal-dependent conformational change provides a structural basis for the inhibition of CTP synthase by gemcitabine-5'-triphosphate. Protein Sci. (2023)

Release Date

2023-05-24

Peptides

CTP synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
AAA

D
BBB

CTP synthase

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