SMTL ID : 4zof.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: G.108, S.120, D.252, E.253 Ligands: MG.2, PRP.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.120, A:E.253, H2O.2, H2O.3 MG.2: 5 residues within 4Å: Chain A: D.112, D.252, E.253 Ligands: MG.1, PRP.3 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.252, A:E.253, H2O.3, H2O.3, H2O.4, H2O.7 MG.6: 6 residues within 4Å: Chain B: G.108, 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.10, H2O.10 MG.7: 5 residues within 4Å: Chain B: D.112, D.252, E.253 Ligands: MG.6, PRP.8 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.252, B:E.253, H2O.10, H2O.10, H2O.10, H2O.14

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, 59L.4 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.108, A:G.111, A:N.118, A:S.120, A:T.121, 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:L.119, A:L.119, A:N.139, A:A.149, A:A.149 Salt bridges: A:K.136 PRP.8: 21 residues within 4Å: Chain B: 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.6, MG.7, 59L.9 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:G.108, B:G.111, B:N.118, B:S.120, B:S.120, B:S.120, B:T.121, B:N.139, B:N.139, B:A.142, B:S.143, B:S.144, B:S.144, B:G.148 Water bridges: B:D.112, B:N.115, B:T.116, B:K.136, B:N.139, B:S.143, B:S.143, B:A.149, B:E.253 Salt bridges: B:K.136

2 x 59L: 2-[(2-carboxy-5-nitrophenyl)amino]-3-methylbenzoic acid(Non-covalent)

59L.4: 15 residues within 4Å: Chain A: V.107, G.108, T.109, H.137, G.138, N.139, A.180, P.181, H.184, Y.187, R.194, N.204, G.207, T.210 Ligands: PRP.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:N.139, A:A.180, A:H.184 Hydrogen bonds: A:T.109, A:N.139 Water bridges: A:Y.187, A:R.194, A:R.194, A:R.194, A:N.204, A:N.204, A:G.207 Salt bridges: A:R.194, A:R.194 pi-Stacking: A:Y.187 59L.9: 15 residues within 4Å: Chain B: V.107, G.108, T.109, H.137, G.138, N.139, A.180, P.181, H.184, Y.187, R.194, N.204, G.207, T.210 Ligands: PRP.8 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:N.139, B:A.180, B:H.184, B:Y.187 Hydrogen bonds: B:N.139, B:R.194, B:N.204, B:N.204 Water bridges: B:R.194, B:G.207, B:G.207 Salt bridges: B:R.194, B:R.194

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.5: 7 residues within 4Å: Chain A: L.306, G.307, G.308, I.352, D.353, G.355, E.358 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.306 Water bridges: A:G.355

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

PO4.10: 8 residues within 4Å: Chain B: R.216, R.239, S.240, S.241, A.266, A.267, G.330, L.331 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.216, B:S.240, B:S.241, B:A.267, B:G.268

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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