SMTL ID : 7dpt.1

Structural basis for ligand binding modes of CTP synthase

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 15 residues within 4Å: Chain A: G.48, T.49, F.50, S.51, P.52, K.306, Y.307, F.373, G.374, R.376, R.479, R.481 Chain C: L.107, G.108 Ligands: MG.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.51, A:Y.307, A:F.373, A:R.479, A:R.481 Water bridges: A:R.479 Salt bridges: A:K.306, A:K.306, A:R.376 GTP.9: 15 residues within 4Å: Chain B: G.48, T.49, F.50, S.51, P.52, K.306, Y.307, F.373, G.374, R.376, R.479, R.481 Chain D: L.107, G.108 Ligands: MG.12 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.51, B:Y.307, B:F.373, B:R.479, B:R.481 Water bridges: B:R.479 Salt bridges: B:K.306, B:K.306, B:R.376 GTP.15: 15 residues within 4Å: Chain A: L.107, G.108 Chain C: G.48, T.49, F.50, S.51, P.52, K.306, Y.307, F.373, G.374, R.376, R.479, R.481 Ligands: MG.18 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.51, C:F.373, C:R.479, C:R.481 Water bridges: C:R.479 Salt bridges: C:K.306, C:K.306, C:R.376 GTP.23: 15 residues within 4Å: Chain B: L.107, G.108 Chain D: G.48, T.49, F.50, S.51, P.52, K.306, Y.307, F.373, G.374, R.376, R.479, R.481 Ligands: MG.26 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:S.51, D:F.373, D:R.479, D:R.481 Water bridges: D:R.479 Salt bridges: D:K.306, D:K.306, D:R.376

4 x DON: 6-DIAZENYL-5-OXO-L-NORLEUCINE(Covalent)

DON.2: 11 residues within 4Å: Chain A: G.372, F.373, C.399, Q.403, E.423, R.479, H.480, R.481, Y.482, Q.524, H.526 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.373 Hydrogen bonds: A:G.372, A:G.372, A:C.399, A:Q.403, A:R.481, A:Y.482 DON.10: 11 residues within 4Å: Chain B: G.372, F.373, C.399, Q.403, E.423, R.479, H.480, R.481, Y.482, Q.524, H.526 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.373 Hydrogen bonds: B:G.372, B:G.372, B:C.399, B:Q.403, B:R.481, B:Y.482 DON.16: 11 residues within 4Å: Chain C: G.372, F.373, C.399, Q.403, E.423, R.479, H.480, R.481, Y.482, Q.524, H.526 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.373 Hydrogen bonds: C:G.372, C:G.372, C:Q.403, C:R.481, C:Y.482 DON.24: 11 residues within 4Å: Chain D: G.372, F.373, C.399, Q.403, E.423, R.479, H.480, R.481, Y.482, Q.524, H.526 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.373 Hydrogen bonds: D:G.372, D:G.372, D:Q.403, D:R.481, D:Y.482

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

ADP.3: 18 residues within 4Å: Chain A: G.13, V.14, G.15, K.16, G.17, V.18, L.69, D.70, E.145, R.216, I.243, H.244, D.245, L.246, D.312 Chain B: A.187 Ligands: MG.6, 5ZL.8 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.13, A:V.14, A:G.15, A:K.16, A:G.17, A:V.18, A:D.70, A:R.216, A:H.244, A:L.246, A:D.312 Salt bridges: A:K.16 ADP.11: 18 residues within 4Å: Chain A: A.187 Chain B: G.13, V.14, G.15, K.16, G.17, V.18, L.69, D.70, E.145, R.216, I.243, H.244, D.245, L.246, D.312 Ligands: MG.13, 5ZL.14 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.13, B:V.14, B:G.15, B:K.16, B:G.17, B:V.18, B:D.70, B:R.216, B:H.244, B:L.246, B:D.312 Salt bridges: B:K.16 ADP.17: 18 residues within 4Å: Chain C: G.13, V.14, G.15, K.16, G.17, V.18, L.69, D.70, E.145, R.216, I.243, H.244, D.245, L.246, D.312 Chain D: A.187 Ligands: MG.20, 5ZL.22 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:G.13, C:V.14, C:G.15, C:K.16, C:G.17, C:V.18, C:D.70, C:E.145, C:R.216, C:H.244, C:D.245, C:L.246, C:D.312 Salt bridges: C:K.16 ADP.25: 18 residues within 4Å: Chain C: A.187 Chain D: G.13, V.14, G.15, K.16, G.17, V.18, L.69, D.70, E.145, R.216, I.243, H.244, D.245, L.246, D.312 Ligands: MG.27, 5ZL.28 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:G.13, D:V.14, D:G.15, D:K.16, D:G.17, D:V.18, D:D.70, D:E.145, D:R.216, D:H.244, D:D.245, D:L.246, D:D.312 Salt bridges: D:K.16

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

MG.4: 1 residues within 4Å: Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain A: E.54 Chain B: K.228 Ligands: 5ZL.8 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain A: G.13 Ligands: ADP.3, 5ZL.8 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain A: K.228 Chain B: E.54 Ligands: 5ZL.14 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Ligands: GTP.9 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain B: G.13 Ligands: ADP.11, 5ZL.14 No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Ligands: GTP.15 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain C: E.54 Chain D: K.228 Ligands: 5ZL.22 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain C: G.13 Ligands: ADP.17, 5ZL.22 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain C: K.228 Chain D: E.54 Ligands: 5ZL.28 No protein-ligand interaction detected (PLIP) MG.26: 1 residues within 4Å: Ligands: GTP.23 No protein-ligand interaction detected (PLIP) MG.27: 3 residues within 4Å: Chain D: G.13 Ligands: ADP.25, 5ZL.28 No protein-ligand interaction detected (PLIP)

4 x 5ZL: [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(2-oxidanyl-4-phosphonooxy-pyrimidin-1-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate

5ZL.8: 24 residues within 4Å: Chain A: S.12, K.16, K.38, D.40, P.41, Y.42, H.55, D.70, E.145, G.147, G.148, D.152, E.154 Chain B: P.191, K.192, T.193, K.194, Q.197, K.228 Chain C: T.110, Q.112 Ligands: ADP.3, MG.5, MG.6 27 PLIP interactions: 14 interactions with chain A, 12 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:S.12, A:Y.42, A:G.148, A:D.152, A:D.152, A:E.154, A:E.154, B:T.193, B:T.193, B:K.194, B:Q.197 Water bridges: A:S.12, A:H.55, A:T.149, B:K.192, B:K.194, C:Q.112 Salt bridges: A:K.16, A:K.38, A:H.55, B:K.192, B:K.192, B:K.194, B:K.194, B:K.228, B:K.228 pi-Stacking: A:H.55 5ZL.14: 24 residues within 4Å: Chain A: P.191, K.192, T.193, K.194, Q.197, K.228 Chain B: S.12, K.16, K.38, D.40, P.41, Y.42, H.55, D.70, E.145, G.147, G.148, D.152, E.154 Chain D: T.110, Q.112 Ligands: MG.7, ADP.11, MG.13 27 PLIP interactions: 14 interactions with chain B, 12 interactions with chain A, 1 interactions with chain D Hydrogen bonds: B:S.12, B:Y.42, B:G.148, B:D.152, B:D.152, B:E.154, B:E.154, A:T.193, A:T.193, A:K.194, A:Q.197 Water bridges: B:S.12, B:H.55, B:T.149, A:K.192, A:K.194, D:Q.112 Salt bridges: B:K.16, B:K.38, B:H.55, A:K.192, A:K.192, A:K.194, A:K.194, A:K.228, A:K.228 pi-Stacking: B:H.55 5ZL.22: 24 residues within 4Å: Chain A: T.110, Q.112 Chain C: S.12, K.16, K.38, D.40, P.41, Y.42, H.55, D.70, E.145, G.147, G.148, D.152, E.154 Chain D: P.191, K.192, T.193, K.194, Q.197, K.228 Ligands: ADP.17, MG.19, MG.20 27 PLIP interactions: 1 interactions with chain A, 13 interactions with chain C, 13 interactions with chain D Water bridges: A:Q.112, C:S.12, C:T.149, D:K.192, D:K.194 Hydrogen bonds: C:S.12, C:D.40, C:Y.42, C:D.68, C:G.148, C:D.152, C:E.154, D:T.193, D:T.193, D:T.193, D:K.194, D:Q.197 Salt bridges: C:K.16, C:K.38, C:H.55, D:K.192, D:K.192, D:K.194, D:K.194, D:K.228, D:K.228 pi-Stacking: C:H.55 5ZL.28: 24 residues within 4Å: Chain B: T.110, Q.112 Chain C: P.191, K.192, T.193, K.194, Q.197, K.228 Chain D: S.12, K.16, K.38, D.40, P.41, Y.42, H.55, D.70, E.145, G.147, G.148, D.152, E.154 Ligands: MG.21, ADP.25, MG.27 27 PLIP interactions: 13 interactions with chain D, 13 interactions with chain C, 1 interactions with chain B Hydrogen bonds: D:S.12, D:D.40, D:Y.42, D:D.68, D:G.148, D:D.152, D:E.154, C:T.193, C:T.193, C:T.193, C:K.194, C:Q.197 Water bridges: D:S.12, D:T.149, C:K.192, C:K.194, B:Q.112 Salt bridges: D:K.16, D:K.38, D:H.55, C:K.192, C:K.192, C:K.194, C:K.194, C:K.228, C:K.228 pi-Stacking: D:H.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, X. et al., Structural basis for ligand binding modes of CTP synthase. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-09-15

Peptides

CTP synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

CTP synthase