SMTL ID : 8fv6.1

E coli. CTP synthase in complex with dF-dCTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

4 x MLA: MALONIC ACID(Non-covalent)

MLA.1: 5 residues within 4Å: Chain A: S.14, S.15, L.16, G.17, K.18 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.15, A:L.16, A:G.17, A:K.18 Water bridges: A:S.14, A:K.18, A:G.19, A:G.19, A:K.40, A:K.40, A:K.40, A:D.72 Salt bridges: A:K.18, A:K.18 MLA.6: 5 residues within 4Å: Chain B: S.14, S.15, L.16, G.17, K.18 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.14, B:S.15, B:L.16, B:G.17, B:K.18 Water bridges: B:S.14, B:K.18, B:G.19, B:G.19, B:K.40 Salt bridges: B:K.18, B:K.18 MLA.7: 5 residues within 4Å: Chain C: S.14, S.15, L.16, G.17, K.18 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:S.15, C:L.16, C:G.17, C:K.18 Water bridges: C:S.14, C:K.18, C:G.19, C:G.19, C:K.40, C:K.40, C:K.40, C:D.72 Salt bridges: C:K.18, C:K.18 MLA.12: 5 residues within 4Å: Chain D: S.14, S.15, L.16, G.17, K.18 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:S.14, D:S.15, D:L.16, D:G.17, D:K.18 Water bridges: D:S.14, D:K.18, D:G.19, D:G.19, D:K.40 Salt bridges: D:K.18, D:K.18

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

GTF.2: 14 residues within 4Å: Chain A: 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, V.115, I.116 Ligands: NA.3 39 PLIP interactions: 27 interactions with chain A, 5 interactions with chain D, 7 interactions with chain B Hydrophobic interactions: A:F.227, D:I.116 Hydrogen bonds: A:T.188, A:T.188, A:T.188, A:K.189, A:K.189, A:Q.192, D:Q.114, B:S.14, B:S.14, B:I.148, B:E.149 Water bridges: A:K.187, A:K.187, A:K.187, A:K.189, A:Q.192, A:Q.192, A:K.196, A:K.196, A:K.196, A:K.223, A:K.223, A:K.223, A:K.223, D:Q.114, D:Q.114, D:V.115, B:S.14, B:E.149, B:E.149 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: 14 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, F.227 Chain C: Q.114, V.115, I.116 Ligands: NA.5 37 PLIP interactions: 29 interactions with chain B, 6 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: B:F.227, C:I.116 Hydrogen bonds: B:T.188, B:K.189, B:K.189, B:Q.192, A:S.14, A:D.147, A:I.148, A:E.149, C:Q.114 Water bridges: B:E.185, B:E.185, B:E.185, B:E.185, B:K.187, B:K.187, B:K.189, B:Q.192, B:K.196, B:K.196, B:K.196, B:K.196, B:K.196, B:E.220, B:K.223, B:K.223, B:K.223, B:K.223, A:D.147, A:E.149 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: K.187, T.188, K.189, Q.192, K.223, F.227 Chain D: S.14, D.147, I.148, E.149 Ligands: NA.9 39 PLIP interactions: 5 interactions with chain B, 27 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: B:I.116, C:F.227 Hydrogen bonds: B:Q.114, C:T.188, C:T.188, C:T.188, C:K.189, C:K.189, C:Q.192, D:S.14, D:S.14, D:I.148, D:E.149 Water bridges: B:Q.114, B:Q.114, B:V.115, C:K.187, C:K.187, C:K.187, C:K.189, C:Q.192, C:Q.192, C:K.196, C:K.196, C:K.196, C:K.223, C:K.223, C:K.223, C:K.223, D:S.14, D:E.149, D:E.149 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: 14 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, F.227 Ligands: NA.11 37 PLIP interactions: 29 interactions with chain D, 6 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: D:F.227, A:I.116 Hydrogen bonds: D:T.188, D:K.189, D:K.189, D:Q.192, C:S.14, C:D.147, C:I.148, C:E.149, A:Q.114 Water bridges: D:E.185, D:E.185, D:E.185, D:E.185, D:K.187, D:K.187, D:K.189, D:Q.192, D:K.196, D:K.196, D:K.196, D:K.196, D:K.196, D:E.220, D:K.223, D:K.223, D:K.223, D:K.223, C:D.147, C:E.149 Salt bridges: D:K.187, D:K.187, 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.187 Ligands: GTF.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.223, A:K.223 Water bridges: A:K.187 NA.5: 2 residues within 4Å: Chain B: K.223 Ligands: GTF.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.223, B:K.223 NA.9: 2 residues within 4Å: Chain C: K.187 Ligands: GTF.8 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.223, C:K.223 Water bridges: C:K.187 NA.11: 2 residues within 4Å: Chain D: K.223 Ligands: GTF.10 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: 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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