SMTL ID : 4zdk.2 (1 other biounit)

Crystal structure of the M. tuberculosis CTP synthase PyrG in complex with UTP, AMP-PCP and oxonorleucine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.49 Å

Oligo State

homo-tetramer

Ligands

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

ONL.1: 12 residues within 4Å: Chain A: G.365, G.366, F.367, C.393, L.394, Q.397, E.416, R.475, H.476, R.477, Y.478, H.524 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.394, A:H.476 Hydrogen bonds: A:G.366, A:Q.397, A:E.416, A:R.477, A:Y.478 ONL.5: 12 residues within 4Å: Chain B: G.365, G.366, F.367, C.393, L.394, Q.397, E.416, R.475, H.476, R.477, Y.478, H.524 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.394, B:H.476 Hydrogen bonds: B:G.366, B:Q.397, B:E.416, B:R.477, B:Y.478 ONL.9: 12 residues within 4Å: Chain C: G.365, G.366, F.367, C.393, L.394, Q.397, E.416, R.475, H.476, R.477, Y.478, H.524 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.367 Hydrogen bonds: C:G.366, C:L.394, C:Q.397, C:E.416, C:R.477, C:Y.478 ONL.13: 12 residues within 4Å: Chain D: G.365, G.366, F.367, C.393, L.394, Q.397, E.416, R.475, H.476, R.477, Y.478, H.524 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.367 Hydrogen bonds: D:G.366, D:L.394, D:Q.397, D:E.416, D:R.477, D:Y.478

4 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.2: 17 residues within 4Å: Chain A: S.21, L.22, G.23, K.24, G.25, L.26, K.46, D.78, E.152, R.223, P.251, D.252, A.253, I.256, I.259 Chain D: P.194 Ligands: MG.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.21, A:L.22, A:G.23, A:K.24, A:G.25, A:L.26, A:K.46, A:R.223, A:P.251, A:A.253 ACP.6: 17 residues within 4Å: Chain B: S.21, L.22, G.23, K.24, G.25, L.26, K.46, D.78, E.152, R.223, P.251, D.252, A.253, I.256, I.259 Chain C: P.194 Ligands: MG.8 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.21, B:L.22, B:G.23, B:K.24, B:G.25, B:L.26, B:K.46, B:R.223, B:P.251, B:A.253 ACP.10: 15 residues within 4Å: Chain B: P.194 Chain C: S.21, L.22, G.23, K.24, G.25, L.26, K.46, D.78, E.152, R.223, D.252, A.253, I.259 Ligands: MG.12 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:S.21, C:L.22, C:G.23, C:K.24, C:G.25, C:L.26, C:K.46, C:K.46, C:R.223, C:R.223, C:A.253 ACP.14: 15 residues within 4Å: Chain A: P.194 Chain D: S.21, L.22, G.23, K.24, G.25, L.26, K.46, D.78, E.152, R.223, D.252, A.253, I.259 Ligands: MG.16 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:S.21, D:L.22, D:G.23, D:K.24, D:G.25, D:L.26, D:K.46, D:K.46, D:R.223, D:R.223, D:A.253

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

UTP.3: 12 residues within 4Å: Chain A: S.20, D.159, I.160, E.161 Chain B: Q.120, V.121, I.122 Chain D: L.198, K.199, T.200, K.201, Q.204 12 PLIP interactions: 2 interactions with chain B, 6 interactions with chain D, 4 interactions with chain A Hydrogen bonds: B:V.121, B:I.122, D:T.200, D:K.201, D:K.201, D:Q.204, A:S.20, A:S.20, A:I.160, A:E.161 Salt bridges: D:K.201, D:K.201 UTP.7: 12 residues within 4Å: Chain A: Q.120, V.121, I.122 Chain B: S.20, D.159, I.160, E.161 Chain C: L.198, K.199, T.200, K.201, Q.204 12 PLIP interactions: 4 interactions with chain B, 6 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:S.20, B:S.20, B:I.160, B:E.161, C:T.200, C:K.201, C:K.201, C:Q.204, A:V.121, A:I.122 Salt bridges: C:K.201, C:K.201 UTP.11: 12 residues within 4Å: Chain B: L.198, K.199, T.200, K.201, Q.204 Chain C: S.20, D.159, I.160, E.161 Chain D: Q.120, V.121, I.122 15 PLIP interactions: 6 interactions with chain C, 6 interactions with chain B, 3 interactions with chain D Hydrogen bonds: C:S.20, C:S.20, C:D.159, C:I.160, C:E.161, C:E.161, B:T.200, B:K.201, B:K.201, B:Q.204, D:Q.120, D:V.121, D:I.122 Salt bridges: B:K.201, B:K.201 UTP.15: 12 residues within 4Å: Chain A: L.198, K.199, T.200, K.201, Q.204 Chain C: Q.120, V.121, I.122 Chain D: S.20, D.159, I.160, E.161 15 PLIP interactions: 6 interactions with chain D, 6 interactions with chain A, 3 interactions with chain C Hydrogen bonds: D:S.20, D:S.20, D:D.159, D:I.160, D:E.161, D:E.161, A:T.200, A:K.201, A:K.201, A:Q.204, C:Q.120, C:V.121, C:I.122 Salt bridges: A:K.201, A:K.201

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: G.25, D.78, E.152 Ligands: ACP.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.78, A:D.78, A:E.152, A:E.152 MG.8: 4 residues within 4Å: Chain B: G.25, D.78, E.152 Ligands: ACP.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.78, B:D.78, B:E.152, B:E.152 MG.12: 4 residues within 4Å: Chain C: G.25, D.78, E.152 Ligands: ACP.10 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.78, C:E.152 MG.16: 4 residues within 4Å: Chain D: G.25, D.78, E.152 Ligands: ACP.14 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.78, D:E.152

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
B

D
B

CTP synthase

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