SMTL ID : 8fvc.1

E coli. CTP synthase in complex with dF-dCTP (potassium malonate + 5 mM MgCl2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-tetramer

Ligands

8 x MLA: MALONIC ACID(Non-covalent)

MLA.1: 6 residues within 4Å: Chain A: S.14, S.15, L.16, G.17, K.18, D.72 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:L.16, A:G.17, A:K.18 Water bridges: A:G.19, A:G.19, A:G.19, A:K.40 Salt bridges: A:K.18, A:K.40 MLA.2: 4 residues within 4Å: Chain A: K.297, G.354, Y.355, R.356 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.354, A:R.356 Salt bridges: A:K.297, A:K.297, A:R.356 MLA.4: 6 residues within 4Å: Chain B: S.14, S.15, L.16, G.17, K.18, D.72 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:L.16, B:G.17, B:K.18, B:D.72 Water bridges: B:G.19, B:G.19, B:G.19, B:K.40 Salt bridges: B:K.18 MLA.5: 5 residues within 4Å: Chain B: K.297, F.353, G.354, Y.355, R.356 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.354, B:R.356 Salt bridges: B:K.297, B:K.297, B:R.356 MLA.7: 6 residues within 4Å: Chain C: S.14, S.15, L.16, G.17, K.18, D.72 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:L.16, C:G.17, C:K.18 Water bridges: C:G.19, C:G.19, C:G.19, C:K.40 Salt bridges: C:K.18, C:K.40 MLA.8: 4 residues within 4Å: Chain C: K.297, G.354, Y.355, R.356 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.354, C:R.356 Salt bridges: C:K.297, C:K.297, C:R.356 MLA.10: 6 residues within 4Å: Chain D: S.14, S.15, L.16, G.17, K.18, D.72 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:L.16, D:G.17, D:K.18, D:D.72 Water bridges: D:G.19, D:G.19, D:G.19, D:K.40 Salt bridges: D:K.18 MLA.11: 5 residues within 4Å: Chain D: K.297, F.353, G.354, Y.355, R.356 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.354, D:R.356 Salt bridges: D:K.297, D:K.297, D:R.356

4 x GTF: 2'-deoxy-2',2'-difluorocytidine 5'-(tetrahydrogen triphosphate)(Non-covalent)

GTF.3: 12 residues within 4Å: Chain A: K.187, T.188, K.189, Q.192, K.223 Chain B: S.14, D.147, I.148, E.149 Chain D: Q.114, V.115, I.116 21 PLIP interactions: 14 interactions with chain A, 5 interactions with chain B, 2 interactions with chain D Hydrogen bonds: A:T.188, A:K.189, A:K.189, A:Q.192, B:S.14, B:D.147, B:I.148, B:E.149, D:Q.114 Water bridges: A:K.187, A:K.187, A:K.223, A:K.223, B:S.14, D:V.115 Salt bridges: A:K.187, A:K.187, A:K.189, A:K.189, A:K.223, A:K.223 GTF.6: 12 residues within 4Å: Chain A: S.14, D.147, I.148, E.149 Chain B: K.187, T.188, K.189, Q.192, K.223 Chain C: Q.114, V.115, I.116 25 PLIP interactions: 3 interactions with chain C, 17 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: C:I.116 Hydrogen bonds: C:Q.114, B:T.188, B:T.188, B:K.189, B:K.189, B:Q.192, A:S.14, A:S.14, A:I.148, A:E.149 Water bridges: C:V.115, B:K.187, B:K.187, B:K.189, B:Q.192, B:K.223, B:K.223, A:E.149 Salt bridges: B:K.187, B:K.187, B:K.189, B:K.189, B:K.223, B:K.223 GTF.9: 12 residues within 4Å: Chain B: Q.114, V.115, I.116 Chain C: K.187, T.188, K.189, Q.192, K.223 Chain D: S.14, D.147, I.148, E.149 21 PLIP interactions: 14 interactions with chain C, 2 interactions with chain B, 5 interactions with chain D Hydrogen bonds: C:T.188, C:K.189, C:K.189, C:Q.192, B:Q.114, D:S.14, D:D.147, D:I.148, D:E.149 Water bridges: C:K.187, C:K.187, C:K.223, C:K.223, B:V.115, D:S.14 Salt bridges: C:K.187, C:K.187, C:K.189, C:K.189, C:K.223, C:K.223 GTF.12: 12 residues within 4Å: Chain A: Q.114, V.115, I.116 Chain C: S.14, D.147, I.148, E.149 Chain D: K.187, T.188, K.189, Q.192, K.223 25 PLIP interactions: 3 interactions with chain A, 5 interactions with chain C, 17 interactions with chain D Hydrophobic interactions: A:I.116 Hydrogen bonds: A:Q.114, C:S.14, C:S.14, C:I.148, C:E.149, D:T.188, D:T.188, D:K.189, D:K.189, D:Q.192 Water bridges: A:V.115, C:E.149, D:K.187, D:K.187, D:K.189, D:Q.192, D:K.223, D:K.223 Salt bridges: D:K.187, D:K.187, D:K.189, D:K.189, D:K.223, D:K.223

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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