SMTL ID : 4zdj.1

Crystal structure of the M. tuberculosis CTP synthase PyrG in complex with two UTP molecules

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-tetramer

Ligands

8 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)

UTP.1: 14 residues within 4Å: Chain A: S.21, D.160, I.161, E.162 Chain B: Q.121, V.122, I.123 Chain C: K.200, T.201, K.202, Q.205, K.236, M.240 Ligands: MG.3 28 PLIP interactions: 7 interactions with chain A, 17 interactions with chain C, 4 interactions with chain B Hydrogen bonds: A:S.21, A:S.21, A:I.161, A:E.162, C:T.201, C:K.202, C:K.202, C:Q.205, B:Q.121, B:V.122, B:I.123 Water bridges: A:G.159, A:E.162, A:E.162, C:K.200, C:K.200, C:K.236, C:K.236, C:K.236, C:K.236, C:K.236 Salt bridges: C:K.200, C:K.200, C:K.202, C:K.202, C:K.236, C:K.236 Hydrophobic interactions: B:I.123 UTP.2: 17 residues within 4Å: Chain A: S.21, S.22, L.23, G.24, K.25, G.26, L.27, T.28, E.153, R.224, T.251, D.253, A.254, I.257, I.260 Chain C: P.195 Ligands: MG.4 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.260 Hydrogen bonds: A:S.22, A:L.23, A:G.24, A:K.25, A:G.26, A:L.27, A:R.224, A:A.254 Water bridges: A:S.21, A:K.25, A:K.25, A:D.79, A:E.153, A:P.252, A:A.254 Salt bridges: A:K.25 pi-Cation interactions: A:R.224 UTP.6: 14 residues within 4Å: Chain A: Q.121, V.122, I.123 Chain B: S.21, D.160, I.161, E.162 Chain D: K.200, T.201, K.202, Q.205, K.236, M.240 Ligands: MG.8 28 PLIP interactions: 4 interactions with chain A, 17 interactions with chain D, 7 interactions with chain B Hydrophobic interactions: A:I.123 Hydrogen bonds: A:Q.121, A:V.122, A:I.123, D:T.201, D:K.202, D:K.202, D:Q.205, B:S.21, B:S.21, B:I.161, B:E.162 Water bridges: D:K.200, D:K.200, D:K.236, D:K.236, D:K.236, D:K.236, D:K.236, B:G.159, B:E.162, B:E.162 Salt bridges: D:K.200, D:K.200, D:K.202, D:K.202, D:K.236, D:K.236 UTP.7: 17 residues within 4Å: Chain B: S.21, S.22, L.23, G.24, K.25, G.26, L.27, T.28, E.153, R.224, T.251, D.253, A.254, I.257, I.260 Chain D: P.195 Ligands: MG.9 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.260 Hydrogen bonds: B:S.22, B:L.23, B:G.24, B:K.25, B:G.26, B:L.27, B:R.224, B:A.254 Water bridges: B:S.21, B:K.25, B:K.25, B:D.79, B:E.153, B:P.252, B:A.254 Salt bridges: B:K.25 pi-Cation interactions: B:R.224 UTP.11: 14 residues within 4Å: Chain A: K.200, T.201, K.202, Q.205, K.236, M.240 Chain C: S.21, D.160, I.161, E.162 Chain D: Q.121, V.122, I.123 Ligands: MG.13 29 PLIP interactions: 17 interactions with chain A, 4 interactions with chain D, 8 interactions with chain C Hydrogen bonds: A:T.201, A:K.202, A:K.202, A:Q.205, D:Q.121, D:V.122, D:I.123, C:S.21, C:S.21, C:D.160, C:I.161, C:E.162 Water bridges: A:K.200, A:K.200, A:K.236, A:K.236, A:K.236, A:K.236, A:K.236, C:G.159, C:E.162, C:E.162 Salt bridges: A:K.200, A:K.200, A:K.202, A:K.202, A:K.236, A:K.236 Hydrophobic interactions: D:I.123 UTP.12: 17 residues within 4Å: Chain A: P.195 Chain C: S.21, S.22, L.23, G.24, K.25, G.26, L.27, T.28, E.153, R.224, T.251, D.253, A.254, I.257, I.260 Ligands: MG.14 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:I.260 Hydrogen bonds: C:S.22, C:L.23, C:G.24, C:K.25, C:G.26, C:L.27, C:R.224, C:A.254 Water bridges: C:S.21, C:K.25, C:K.25, C:D.79, C:P.252, C:A.254 Salt bridges: C:K.25 pi-Cation interactions: C:R.224 UTP.16: 14 residues within 4Å: Chain B: K.200, T.201, K.202, Q.205, K.236, M.240 Chain C: Q.121, V.122, I.123 Chain D: S.21, D.160, I.161, E.162 Ligands: MG.18 29 PLIP interactions: 17 interactions with chain B, 8 interactions with chain D, 4 interactions with chain C Hydrogen bonds: B:T.201, B:K.202, B:K.202, B:Q.205, D:S.21, D:S.21, D:D.160, D:I.161, D:E.162, C:Q.121, C:V.122, C:I.123 Water bridges: B:K.200, B:K.200, B:K.236, B:K.236, B:K.236, B:K.236, B:K.236, D:G.159, D:E.162, D:E.162 Salt bridges: B:K.200, B:K.200, B:K.202, B:K.202, B:K.236, B:K.236 Hydrophobic interactions: C:I.123 UTP.17: 17 residues within 4Å: Chain B: P.195 Chain D: S.21, S.22, L.23, G.24, K.25, G.26, L.27, T.28, E.153, R.224, T.251, D.253, A.254, I.257, I.260 Ligands: MG.19 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:I.260 Hydrogen bonds: D:S.22, D:L.23, D:G.24, D:K.25, D:G.26, D:L.27, D:R.224, D:A.254 Water bridges: D:S.21, D:K.25, D:K.25, D:D.79, D:P.252, D:A.254 Salt bridges: D:K.25 pi-Cation interactions: D:R.224

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain C: K.236 Ligands: UTP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: D.79 Ligands: UTP.2 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain D: K.236 Ligands: UTP.6 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain B: D.79 Ligands: UTP.7 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain A: K.236 Ligands: UTP.11 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain C: D.79 Ligands: UTP.12 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain B: K.236 Ligands: UTP.16 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain D: D.79 Ligands: UTP.17 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: P.61, F.62, E.66, A.317, Y.318, G.366, G.367, F.368, I.370 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.317, A:F.368 Water bridges: A:F.368 GOL.10: 9 residues within 4Å: Chain B: P.61, F.62, E.66, A.317, Y.318, G.366, G.367, F.368, I.370 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.317, B:F.368 Water bridges: B:F.368 GOL.15: 9 residues within 4Å: Chain C: P.61, F.62, E.66, A.317, Y.318, G.366, G.367, F.368, I.370 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.317, C:F.368 Water bridges: C:F.368 GOL.20: 9 residues within 4Å: Chain D: P.61, F.62, E.66, A.317, Y.318, G.366, G.367, F.368, I.370 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.317, D:F.368 Water bridges: D:F.368

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mori, G. et al., Thiophenecarboxamide Derivatives Activated by EthA Kill Mycobacterium tuberculosis by Inhibiting the CTP Synthetase PyrG. Chem.Biol. (2015)

Release Date

2015-07-01

Peptides

CTP synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

CTP synthase

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