SMTL ID : 8fvd.1

E coli. CTP synthase in complex with dF-dCTP (potassium malonate + 100 mM MgCl2)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-tetramer

Ligands

4 x MLA: MALONIC ACID(Non-covalent)

MLA.1: 4 residues within 4Å: Chain A: S.14, L.16, G.17, K.18 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.16, A:G.17, A:K.18 Salt bridges: A:K.18 MLA.6: 5 residues within 4Å: Chain B: S.14, S.15, L.16, G.17, K.18 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.14, B:L.16, B:G.17, B:K.18 Water bridges: B:K.18, B:K.18 Salt bridges: B:K.18, B:K.18, B:K.40 MLA.7: 4 residues within 4Å: Chain C: S.14, L.16, G.17, K.18 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.16, C:G.17, C:K.18 Salt bridges: C:K.18 MLA.12: 5 residues within 4Å: Chain D: S.14, S.15, L.16, G.17, K.18 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:S.14, D:L.16, D:G.17, D:K.18 Water bridges: D:K.18, D:K.18 Salt bridges: D:K.18, D:K.18, D:K.40

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

GTF.2: 14 residues within 4Å: Chain A: V.186, 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 Ligands: MG.3 20 PLIP interactions: 14 interactions with chain A, 5 interactions with chain B, 1 interactions with chain D Hydrogen bonds: A:T.188, A:T.188, A:T.188, A:K.189, A:K.189, A:Q.192, B:S.14, B:S.14, B:I.148, B:E.149, D:Q.114 Water bridges: A:K.187, B:S.14 Salt bridges: A:K.187, A:K.187, A:K.189, A:K.189, A:K.189, A:K.223, A:K.223 GTF.4: 15 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, V.115, I.116 Ligands: MG.5 19 PLIP interactions: 4 interactions with chain A, 14 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:S.14, A:D.147, A:I.148, A:E.149, B:T.188, B:K.189, B:K.189, B:Q.192, C:Q.114 Hydrophobic interactions: B:F.227 Water bridges: B:V.186, B:E.220, B:E.220 Salt bridges: B:K.187, B:K.187, B:K.189, B:K.189, B:K.223, B:K.223 GTF.8: 14 residues within 4Å: Chain B: Q.114, V.115, I.116 Chain C: V.186, K.187, T.188, K.189, Q.192, K.223 Chain D: S.14, D.147, I.148, E.149 Ligands: MG.9 20 PLIP interactions: 14 interactions with chain C, 1 interactions with chain B, 5 interactions with chain D Hydrogen bonds: C:T.188, C:T.188, C:T.188, C:K.189, C:K.189, C:Q.192, B:Q.114, D:S.14, D:S.14, D:I.148, D:E.149 Water bridges: C:K.187, D:S.14 Salt bridges: C:K.187, C:K.187, C:K.189, C:K.189, C:K.189, C:K.223, C:K.223 GTF.10: 15 residues within 4Å: Chain A: Q.114, V.115, 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: MG.11 19 PLIP interactions: 4 interactions with chain C, 14 interactions with chain D, 1 interactions with chain A Hydrogen bonds: C:S.14, C:D.147, C:I.148, C:E.149, D:T.188, D:K.189, D:K.189, D:Q.192, A:Q.114 Hydrophobic interactions: D:F.227 Water bridges: D:V.186, D:E.220, D:E.220 Salt bridges: D:K.187, D:K.187, D:K.189, D:K.189, D:K.223, D:K.223

4 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 1 residues within 4Å: Ligands: GTF.2 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Ligands: GTF.4 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: GTF.8 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Ligands: GTF.10 No protein-ligand interaction detected (PLIP)

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
A

B
B

C
A

D
B

CTP synthase

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