SMTL ID : 4zoj.1

Methylsulfanyl-containing inhibitor bound in the active site of Mycobacterium tuberculosis anthranilate phosphoribosyltransferase (AnPRT; trpD)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.112, D.252, E.253 Ligands: MG.2, PRP.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.252, H2O.1, H2O.2, H2O.3, H2O.6 MG.2: 5 residues within 4Å: Chain A: S.120, D.252, E.253 Ligands: MG.1, PRP.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.120, A:E.253, H2O.1, H2O.2 MG.6: 5 residues within 4Å: Chain B: S.120, D.252, E.253 Ligands: MG.7, PRP.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.120, B:E.253, H2O.7, H2O.8 MG.7: 4 residues within 4Å: Chain B: D.252, E.253 Ligands: MG.6, PRP.8 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.252, H2O.7, H2O.9, H2O.10, H2O.11

2 x PRP: 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose(Non-covalent)

PRP.3: 21 residues within 4Å: Chain A: V.107, G.108, G.110, G.111, N.118, L.119, S.120, T.121, K.136, N.139, R.140, A.141, A.142, S.143, S.144, G.147, G.148, E.253 Ligands: MG.1, MG.2, 61L.4 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.108, A:G.111, A:N.118, A:S.120, A:S.120, A:T.121, A:N.139, A:N.139, A:A.142, A:S.143, A:S.144, A:S.144, A:G.148 Water bridges: A:D.112, A:D.112, A:L.119, A:L.119, A:K.136, A:N.139, A:A.149 Salt bridges: A:K.136 PRP.8: 22 residues within 4Å: Chain B: V.107, G.108, G.110, G.111, D.112, N.118, L.119, S.120, T.121, K.136, N.139, R.140, A.141, A.142, S.143, S.144, G.147, G.148, E.253 Ligands: MG.6, MG.7, 61L.9 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:G.108, B:G.111, B:D.112, B:N.118, B:L.119, B:S.120, B:T.121, B:T.121, B:R.140, B:A.142, B:S.143, B:S.144, B:S.144, B:G.148 Water bridges: B:N.139, B:N.139 Salt bridges: B:K.136

2 x 61L: 4-methyl-2-{[2-methyl-6-(methylsulfanyl)phenyl]amino}benzoic acid(Non-covalent)

61L.4: 14 residues within 4Å: Chain A: M.87, T.109, H.137, G.138, N.139, A.180, P.181, H.184, Y.187, A.191, R.194, G.207, T.210 Ligands: PRP.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:N.139, A:A.180, A:H.184, A:Y.187 Hydrogen bonds: A:N.139, A:R.194 Water bridges: A:R.194, A:R.194, A:N.204 Salt bridges: A:R.194 61L.9: 12 residues within 4Å: Chain B: M.87, H.137, G.138, N.139, A.180, P.181, H.184, Y.187, A.191, G.207, T.210 Ligands: PRP.8 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:N.139, B:A.180, B:H.184, B:Y.187 Hydrogen bonds: B:N.139

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 8 residues within 4Å: Chain A: R.216, R.239, S.240, S.241, A.266, A.267, G.330, L.331 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.216, A:A.267, A:G.330 Water bridges: A:G.268, A:G.268

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.10: 6 residues within 4Å: Chain B: L.306, G.307, I.352, D.353, G.355, E.358 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.306 Water bridges: B:G.355

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Evans, G.L. et al., Inhibitor bound in the active site of Mycobacterium tuberculosis anthranilate phosphoribosyltransferase (AnPRT; trpD). To be Published

Release Date

2016-05-11

Peptides

Anthranilate phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Anthranilate phosphoribosyltransferase

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