SMTL ID : 8fv8.1

E coli. CTP synthase in complex with dF-dCTP + ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 12 residues within 4Å: Chain A: S.15, L.16, G.17, I.20, R.211, K.239, D.240, V.241, I.247, D.303, K.306 Chain B: A.182 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.15, A:G.17, A:K.239, A:V.241, A:D.303, A:K.306, A:K.306, B:A.182 Water bridges: A:S.15, A:R.211 ADP.6: 15 residues within 4Å: Chain A: A.182 Chain B: S.15, L.16, G.17, K.18, G.19, I.20, D.72, E.140, R.211, K.239, D.240, V.241, I.247, K.306 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.15, B:L.16, B:G.17, B:K.18, B:G.19, B:D.72, B:E.140, B:R.211, B:K.239, B:D.240, B:V.241, B:K.306, B:K.306 Water bridges: B:K.18, B:K.18, B:E.140, B:D.303, A:A.182 Salt bridges: B:K.18 ADP.7: 12 residues within 4Å: Chain C: S.15, L.16, G.17, I.20, R.211, K.239, D.240, V.241, I.247, D.303, K.306 Chain D: A.182 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.15, C:G.17, C:K.239, C:V.241, C:D.303, C:K.306, C:K.306, D:A.182 Water bridges: C:S.15, C:R.211 ADP.12: 15 residues within 4Å: Chain C: A.182 Chain D: S.15, L.16, G.17, K.18, G.19, I.20, D.72, E.140, R.211, K.239, D.240, V.241, I.247, K.306 19 PLIP interactions: 18 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.15, D:L.16, D:G.17, D:K.18, D:G.19, D:D.72, D:E.140, D:R.211, D:K.239, D:D.240, D:V.241, D:K.306, D:K.306 Water bridges: D:K.18, D:K.18, D:E.140, D:D.303, C:A.182 Salt bridges: D:K.18

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

GTF.2: 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 40 PLIP interactions: 27 interactions with chain B, 4 interactions with chain C, 9 interactions with chain A Hydrophobic interactions: B:F.227, C:I.116 Hydrogen bonds: B:T.188, B:T.188, B:T.188, B:K.189, B:K.189, B:Q.192, C:Q.114, A:S.14, A:S.14, A:S.14, A:I.148, A:E.149 Water bridges: B:K.187, B:K.187, 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:K.223, B:K.223, B:K.223, C:V.115, C:E.155, A:G.146, A:D.147, A:E.149, A:E.149 Salt bridges: B:K.187, B:K.187, B:K.189, B:K.189, B:K.223, B:K.223 GTF.3: 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.4 34 PLIP interactions: 26 interactions with chain A, 4 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: A:F.227, D:I.116 Hydrogen bonds: A:T.188, A:K.189, A:K.189, A:Q.192, D:Q.114, B:S.14, B:D.147, B:I.148, B:E.149 Water bridges: A:E.185, A:E.185, A:K.187, A:K.187, A:K.189, A:Q.192, A:K.196, A:K.196, A:K.196, A:K.196, A:K.223, A:K.223, A:K.223, A:K.223, A:K.223, D:Q.114, D:V.115 Salt bridges: A:K.187, A:K.187, A:K.189, A:K.189, A:K.223, A:K.223 GTF.8: 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 40 PLIP interactions: 4 interactions with chain A, 27 interactions with chain D, 9 interactions with chain C Hydrophobic interactions: A:I.116, D:F.227 Hydrogen bonds: A:Q.114, D:T.188, D:T.188, D:T.188, D:K.189, D:K.189, D:Q.192, C:S.14, C:S.14, C:S.14, C:I.148, C:E.149 Water bridges: A:V.115, A:E.155, D:K.187, D:K.187, 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:K.223, D:K.223, D:K.223, C:G.146, C:D.147, C:E.149, C:E.149 Salt bridges: D:K.187, D:K.187, D:K.189, D:K.189, D:K.223, D:K.223 GTF.9: 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.10 34 PLIP interactions: 4 interactions with chain D, 26 interactions with chain C, 4 interactions with chain B Hydrogen bonds: D:S.14, D:D.147, D:I.148, D:E.149, C:T.188, C:K.189, C:K.189, C:Q.192, B:Q.114 Hydrophobic interactions: C:F.227, B:I.116 Water bridges: C:E.185, C:E.185, C:K.187, C:K.187, C:K.189, C:Q.192, C:K.196, C:K.196, C:K.196, C:K.196, C:K.223, C:K.223, C:K.223, C:K.223, C:K.223, B:Q.114, B:V.115 Salt bridges: C:K.187, C:K.187, C:K.189, C:K.189, C:K.223, C:K.223

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

NA.4: 2 residues within 4Å: Chain A: K.187 Ligands: GTF.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.187 NA.5: 1 residues within 4Å: Ligands: GTF.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.223 Water bridges: B:K.187 NA.10: 2 residues within 4Å: Chain C: K.187 Ligands: GTF.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.187 NA.11: 1 residues within 4Å: Ligands: GTF.8 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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