SMTL ID : 8i9o.1

ecCTPS filament bound with CTP, NADH, DON

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x ADE: ADENINE(Non-covalent)

ADE.1: 9 residues within 4Å: Chain A: L.16, G.17, I.20, R.211, L.238, K.239, D.240, V.241, I.247 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.239, A:V.241 pi-Cation interactions: A:R.211 ADE.7: 9 residues within 4Å: Chain B: L.16, G.17, I.20, R.211, L.238, K.239, D.240, V.241, I.247 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.239, B:V.241 pi-Cation interactions: B:R.211 ADE.9: 9 residues within 4Å: Chain C: L.16, G.17, I.20, R.211, L.238, K.239, D.240, V.241, I.247 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.239, C:D.240, C:V.241 pi-Cation interactions: C:R.211 ADE.15: 9 residues within 4Å: Chain D: L.16, G.17, I.20, R.211, L.238, K.239, D.240, V.241, I.247 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.239, D:D.240, D:V.241 pi-Cation interactions: D:R.211

4 x ONL: 5-OXO-L-NORLEUCINE(Covalent)

ONL.2: 12 residues within 4Å: Chain A: G.351, G.352, F.353, C.379, L.380, Q.383, E.403, R.468, H.469, R.470, Y.471, H.515 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.353, A:H.469 Hydrogen bonds: A:G.352, A:L.380, A:Q.383, A:E.403, A:R.470, A:Y.471 ONL.8: 12 residues within 4Å: Chain B: G.351, G.352, F.353, C.379, L.380, Q.383, E.403, R.468, H.469, R.470, Y.471, H.515 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.353, B:H.469 Hydrogen bonds: B:G.352, B:L.380, B:Q.383, B:E.403, B:R.470, B:Y.471 ONL.10: 12 residues within 4Å: Chain C: G.351, G.352, F.353, C.379, L.380, Q.383, E.403, R.468, H.469, R.470, Y.471, H.515 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.353, C:H.469 Hydrogen bonds: C:G.352, C:L.380, C:Q.383, C:E.403, C:R.470, C:Y.471 ONL.16: 12 residues within 4Å: Chain D: G.351, G.352, F.353, C.379, L.380, Q.383, E.403, R.468, H.469, R.470, Y.471, H.515 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.353, D:H.469 Hydrogen bonds: D:G.352, D:L.380, D:Q.383, D:E.403, D:R.470, D:Y.471

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

CTP.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: MG.4 21 PLIP interactions: 12 interactions with chain A, 5 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: A:F.227, D:I.116 Hydrogen bonds: A:T.188, A:K.189, A:K.189, A:Q.192, B:S.14, B:S.14, B:D.147, B:I.148, B:E.149, D:Q.114, D:V.115, D:I.116 Salt bridges: A:K.187, A:K.187, A:K.189, A:K.189, A:K.223, A:K.223 pi-Cation interactions: A:K.189 CTP.5: 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.6 21 PLIP interactions: 5 interactions with chain A, 4 interactions with chain C, 12 interactions with chain B Hydrogen bonds: A:S.14, A:S.14, A:D.147, A:I.148, A:E.149, C:Q.114, C:V.115, C:I.116, B:T.188, B:K.189, B:K.189, B:Q.192 Hydrophobic interactions: C:I.116, B:F.227 Salt bridges: B:K.187, B:K.187, B:K.189, B:K.189, B:K.223, B:K.223 pi-Cation interactions: B:K.189 CTP.11: 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: MG.12 21 PLIP interactions: 4 interactions with chain B, 12 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: B:I.116, C:F.227 Hydrogen bonds: B:Q.114, B:V.115, B:I.116, 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 Salt bridges: C:K.187, C:K.187, C:K.189, C:K.189, C:K.223, C:K.223 pi-Cation interactions: C:K.189 CTP.13: 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 21 PLIP interactions: 5 interactions with chain C, 12 interactions with chain D, 4 interactions with chain A Hydrogen bonds: C:S.14, C:S.14, C:I.148, C:E.149, C:E.149, D:T.188, D:K.189, D:K.189, D:Q.192, A:Q.114, A:V.115, A:I.116 Hydrophobic interactions: D:F.227, A:I.116 Salt bridges: D:K.187, D:K.187, D:K.189, D:K.189, D:K.223, D:K.223 pi-Cation interactions: D:K.189

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

MG.4: 1 residues within 4Å: Ligands: CTP.3 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Ligands: CTP.5 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Ligands: CTP.11 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Ligands: CTP.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, C. et al., Filamentation and inhibition of prokaryotic CTP synthase with ligands. Mlife (2024)

Release Date

2024-02-14

Peptides

CTP synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

CTP synthase