SMTL ID : 7wj4.1

Structural basis for ligand binding modes of CTP synthase

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

GTP.1: 10 residues within 4Å: Chain A: T.49, F.50, S.51, P.52, Y.53, Y.307, R.376, R.481 Chain C: G.108 Ligands: MG.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.51, A:R.481 Salt bridges: A:R.376 GTP.10: 10 residues within 4Å: Chain B: T.49, F.50, S.51, P.52, Y.53, Y.307, R.376, R.481 Chain D: G.108 Ligands: MG.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.51, B:R.481 Salt bridges: B:R.376 GTP.15: 10 residues within 4Å: Chain A: G.108 Chain C: T.49, F.50, S.51, P.52, Y.53, Y.307, R.376, R.481 Ligands: MG.19 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.51, C:R.481 Salt bridges: C:R.376 GTP.24: 10 residues within 4Å: Chain B: G.108 Chain D: T.49, F.50, S.51, P.52, Y.53, Y.307, R.376, R.481 Ligands: MG.28 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.51, D:R.481 Salt bridges: D:R.376

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 16 residues within 4Å: Chain A: G.13, V.14, G.15, K.16, G.17, V.18, D.70, R.216, I.243, H.244, D.245, L.246, I.249, V.252 Ligands: MG.4, UTP.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:H.244, A:L.246, A:D.312 Salt bridges: A:K.16, A:K.16, A:K.38 ATP.11: 16 residues within 4Å: Chain B: G.13, V.14, G.15, K.16, G.17, V.18, D.70, R.216, I.243, H.244, D.245, L.246, I.249, V.252 Ligands: UTP.6, MG.13 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:H.244, B:L.246, B:D.312 Salt bridges: B:K.16, B:K.16, B:K.38 ATP.16: 16 residues within 4Å: Chain C: G.13, V.14, G.15, K.16, G.17, V.18, D.70, R.216, I.243, H.244, D.245, L.246, I.249, V.252 Ligands: MG.18, UTP.22 12 PLIP interactions: 12 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:H.244, C:L.246, C:D.312 Salt bridges: C:K.16, C:K.16, C:K.38 ATP.25: 16 residues within 4Å: Chain D: G.13, V.14, G.15, K.16, G.17, V.18, D.70, R.216, I.243, H.244, D.245, L.246, I.249, V.252 Ligands: UTP.20, MG.27 12 PLIP interactions: 12 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:H.244, D:L.246, D:D.312 Salt bridges: D:K.16, D:K.16, D:K.38

4 x GGL: GAMMA-L-GLUTAMIC ACID(Non-covalent)

GGL.3: 11 residues within 4Å: Chain A: G.371, G.372, F.373, I.398, C.399, L.400, Q.403, R.479, H.480, R.481, Y.482 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.373, A:L.400 Hydrogen bonds: A:G.372, A:Q.403, A:R.481, A:Y.482 Salt bridges: A:H.526 GGL.12: 11 residues within 4Å: Chain B: G.371, G.372, F.373, I.398, C.399, L.400, Q.403, R.479, H.480, R.481, Y.482 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.373, B:L.400 Hydrogen bonds: B:G.372, B:Q.403, B:R.481, B:Y.482 Salt bridges: B:H.526 GGL.17: 11 residues within 4Å: Chain C: G.371, G.372, F.373, I.398, C.399, L.400, Q.403, R.479, H.480, R.481, Y.482 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.373, C:L.400 Hydrogen bonds: C:G.372, C:C.399, C:Q.403, C:R.481, C:Y.482 Salt bridges: C:H.526 GGL.26: 11 residues within 4Å: Chain D: G.371, G.372, F.373, I.398, C.399, L.400, Q.403, R.479, H.480, R.481, Y.482 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.373, D:L.400 Hydrogen bonds: D:G.372, D:C.399, D:Q.403, D:R.481, D:Y.482 Salt bridges: D:H.526

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

MG.4: 4 residues within 4Å: Chain A: K.38, D.70, E.145 Ligands: ATP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.70, A:E.145 MG.5: 1 residues within 4Å: Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: UTP.6 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: UTP.8 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain B: K.38, D.70, E.145 Ligands: ATP.11 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.70, B:E.145 MG.14: 1 residues within 4Å: Ligands: GTP.10 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain C: K.38, D.70, E.145 Ligands: ATP.16 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.70, C:E.145 MG.19: 1 residues within 4Å: Ligands: GTP.15 No protein-ligand interaction detected (PLIP) MG.21: 1 residues within 4Å: Ligands: UTP.20 No protein-ligand interaction detected (PLIP) MG.23: 1 residues within 4Å: Ligands: UTP.22 No protein-ligand interaction detected (PLIP) MG.27: 4 residues within 4Å: Chain D: K.38, D.70, E.145 Ligands: ATP.25 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.70, D:E.145 MG.28: 1 residues within 4Å: Ligands: GTP.24 No protein-ligand interaction detected (PLIP)

4 x UTP: URIDINE 5'-TRIPHOSPHATE(Covalent)

UTP.6: 16 residues within 4Å: Chain A: K.192, T.193, K.194, Q.197, K.228 Chain B: S.12, K.38, D.40, P.41, Y.42, G.148, D.152, E.154 Chain D: Q.112 Ligands: MG.7, ATP.11 16 PLIP interactions: 8 interactions with chain A, 6 interactions with chain B, 2 interactions with chain D Hydrogen bonds: A:T.193, A:K.194, A:Q.197, B:S.12, B:S.12, B:K.38, B:D.40, B:Y.42, D:T.110, D:Q.112 Salt bridges: A:K.192, A:K.194, A:K.194, A:K.228, A:K.228 pi-Cation interactions: B:H.55 UTP.8: 16 residues within 4Å: Chain A: S.12, K.38, D.40, P.41, Y.42, G.148, D.152, E.154 Chain B: K.192, T.193, K.194, Q.197, K.228 Chain C: Q.112 Ligands: ATP.2, MG.9 16 PLIP interactions: 6 interactions with chain A, 8 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:S.12, A:S.12, A:K.38, A:D.40, A:Y.42, B:T.193, B:K.194, B:Q.197, C:T.110, C:Q.112 pi-Cation interactions: A:H.55 Salt bridges: B:K.192, B:K.194, B:K.194, B:K.228, B:K.228 UTP.20: 16 residues within 4Å: Chain B: Q.112 Chain C: K.192, T.193, K.194, Q.197, K.228 Chain D: S.12, K.38, D.40, P.41, Y.42, G.148, D.152, E.154 Ligands: MG.21, ATP.25 18 PLIP interactions: 10 interactions with chain D, 7 interactions with chain C, 1 interactions with chain B Hydrogen bonds: D:S.12, D:S.12, D:S.12, D:K.38, D:D.40, D:D.40, D:Y.42, D:D.152, D:E.154, C:K.194, C:Q.197, B:Q.112 pi-Cation interactions: D:H.55 Salt bridges: C:K.192, C:K.194, C:K.194, C:K.228, C:K.228 UTP.22: 16 residues within 4Å: Chain A: Q.112 Chain C: S.12, K.38, D.40, P.41, Y.42, G.148, D.152, E.154 Chain D: K.192, T.193, K.194, Q.197, K.228 Ligands: ATP.16, MG.23 18 PLIP interactions: 10 interactions with chain C, 1 interactions with chain A, 7 interactions with chain D Hydrogen bonds: C:S.12, C:S.12, C:S.12, C:K.38, C:D.40, C:D.40, C:Y.42, C:D.152, C:E.154, A:Q.112, D:K.194, D:Q.197 pi-Cation interactions: C:H.55 Salt bridges: D:K.192, D:K.194, D:K.194, D:K.228, D:K.228

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

2023-01-11

Peptides

CTP synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

C
B

D
C

CTP synthase

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