SMTL ID : 8fve.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

6 x MLA: MALONIC ACID(Non-covalent)

MLA.1: 5 residues within 4Å: Chain A: K.297, F.353, G.354, Y.355, R.356 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:R.356 Hydrogen bonds: A:G.354, A:Y.355, A:R.356 Salt bridges: A:K.297, A:K.297, A:R.356 MLA.5: 6 residues within 4Å: Chain B: S.14, S.15, L.16, G.17, K.18, E.140 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.14, B:L.16, B:G.17, B:K.18 Water bridges: B:K.18, B:G.19, B:G.19, B:K.40 Salt bridges: B:K.18, B:K.18 MLA.6: 6 residues within 4Å: Chain B: K.297, Y.298, F.353, G.354, Y.355, R.356 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.356 Salt bridges: B:K.297, B:K.297, B:R.356, B:R.356 MLA.8: 5 residues within 4Å: Chain C: K.297, F.353, G.354, Y.355, R.356 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:R.356 Hydrogen bonds: C:G.354, C:Y.355, C:R.356 Salt bridges: C:K.297, C:K.297, C:R.356 MLA.12: 6 residues within 4Å: Chain D: S.14, S.15, L.16, G.17, K.18, E.140 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:S.14, D:L.16, D:G.17, D:K.18 Water bridges: D:K.18, D:G.19, D:G.19, D:K.40 Salt bridges: D:K.18, D:K.18 MLA.13: 6 residues within 4Å: Chain D: K.297, Y.298, F.353, G.354, Y.355, R.356 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.356 Salt bridges: D:K.297, D:K.297, D:R.356, D:R.356

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

MG.2: 1 residues within 4Å: Ligands: CTP.4 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: K.223 Ligands: CTP.3 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: CTP.11 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain D: K.223 Ligands: CTP.10 No protein-ligand interaction detected (PLIP)

4 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.3: 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: MG.7 31 PLIP interactions: 20 interactions with chain B, 8 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: B:F.227, C:I.116 Hydrogen bonds: B:T.188, B:T.188, B:K.189, B:K.189, B:Q.192, A:S.14, A:D.147, A:I.148, A:E.149, A:E.149, A:E.149, A:E.149, C:V.115, C:I.116 Water bridges: B:K.187, B:K.187, B:K.187, B:Q.192, B:E.220, B:K.223, B:K.223, A:S.14 Salt bridges: B:K.187, B:K.187, B:K.189, B:K.189, B:K.189, B:K.223, B:K.223 CTP.4: 15 residues within 4Å: Chain A: K.187, T.188, K.189, Q.192, K.196, K.223, F.227 Chain B: S.14, D.147, I.148, E.149 Chain D: Q.114, V.115, I.116 Ligands: MG.2 29 PLIP interactions: 18 interactions with chain A, 8 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: A:F.227, D:I.116 Hydrogen bonds: 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, B:E.149, B:E.149, D:V.115, D:I.116 Water bridges: A:K.187, A:K.196, A:K.196, A:K.223, A:K.223, B:S.14, 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 CTP.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: MG.14 31 PLIP interactions: 20 interactions with chain D, 3 interactions with chain A, 8 interactions with chain C Hydrophobic interactions: D:F.227, A:I.116 Hydrogen bonds: D:T.188, D:T.188, D:K.189, D:K.189, D:Q.192, A:V.115, A:I.116, C:S.14, C:D.147, C:I.148, C:E.149, C:E.149, C:E.149, C:E.149 Water bridges: D:K.187, D:K.187, D:K.187, D:Q.192, D:E.220, D:K.223, D:K.223, C:S.14 Salt bridges: D:K.187, D:K.187, D:K.189, D:K.189, D:K.189, D:K.223, D:K.223 CTP.11: 15 residues within 4Å: Chain B: Q.114, V.115, I.116 Chain C: K.187, T.188, K.189, Q.192, K.196, K.223, F.227 Chain D: S.14, D.147, I.148, E.149 Ligands: MG.9 29 PLIP interactions: 18 interactions with chain C, 8 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: C:F.227, B:I.116 Hydrogen bonds: 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, D:E.149, D:E.149, B:V.115, B:I.116 Water bridges: C:K.187, C:K.196, C:K.196, C:K.223, C:K.223, D:S.14, 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

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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