SMTL ID : 4giu.1

Bianthranilate-like analogue bound in inner site of anthranilate phosphoribosyltransferase (AnPRT; trpD).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-dimer

Ligands

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

PRP.1: 21 residues within 4Å: Chain A: V.106, G.107, G.109, G.110, N.117, L.118, S.119, T.120, K.135, N.138, R.139, A.140, A.141, S.142, S.143, G.146, G.147, E.252 Ligands: MG.2, MG.3, 636.4 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:G.107, A:G.110, A:N.117, A:S.119, A:S.119, A:T.120, A:T.120, A:T.120, A:N.138, A:N.138, A:A.141, A:S.142, A:S.143, A:S.143, A:G.147 Water bridges: A:D.111, A:N.114, A:L.118, A:L.118, A:K.135, A:N.138, A:A.148 Salt bridges: A:K.135 PRP.10: 21 residues within 4Å: Chain B: V.106, G.107, G.109, G.110, N.117, L.118, S.119, T.120, K.135, N.138, R.139, A.140, A.141, S.142, S.143, G.146, G.147, E.252 Ligands: MG.11, MG.12, 636.13 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:G.107, B:G.110, B:N.117, B:S.119, B:S.119, B:T.120, B:N.138, B:N.138, B:A.141, B:S.142, B:S.143, B:G.147 Water bridges: B:D.111, B:D.111, B:D.111, B:N.114, B:T.115, B:N.138, B:A.148, B:E.252 Salt bridges: B:K.135

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: G.107, S.119, D.251, E.252 Ligands: PRP.1, MG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.119, A:E.252, H2O.1, H2O.9 MG.3: 5 residues within 4Å: Chain A: D.111, D.251, E.252 Ligands: PRP.1, MG.2 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.251, A:E.252, H2O.4, H2O.9, H2O.9, H2O.9 MG.11: 6 residues within 4Å: Chain B: G.107, S.119, D.251, E.252 Ligands: PRP.10, MG.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.119, B:E.252, H2O.11, H2O.12 MG.12: 5 residues within 4Å: Chain B: D.111, D.251, E.252 Ligands: PRP.10, MG.11 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.251, B:E.252, H2O.12, H2O.14, H2O.16, H2O.19

2 x 636: 2-[(2-carboxy-5-methylphenyl)amino]-3-methylbenzoic acid(Non-covalent)

636.4: 14 residues within 4Å: Chain A: G.107, T.108, H.136, G.137, N.138, A.179, P.180, H.183, Y.186, R.193, N.203, G.206, T.209 Ligands: PRP.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:N.138, A:A.179, A:H.183 Hydrogen bonds: A:T.108, A:N.138, A:N.138 Water bridges: A:R.139, A:Y.186, A:R.193, A:R.193, A:R.193, A:N.203, A:N.203, A:G.206 Salt bridges: A:R.193, A:R.193 pi-Stacking: A:Y.186 636.13: 15 residues within 4Å: Chain B: M.86, G.107, T.108, H.136, G.137, N.138, A.179, P.180, H.183, Y.186, R.193, N.203, G.206, T.209 Ligands: PRP.10 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:N.138, B:A.179, B:H.183 Hydrogen bonds: B:N.138, B:N.138, B:N.203 Water bridges: B:Y.186, B:R.193, B:R.193, B:R.193, B:R.193, B:G.206 Salt bridges: B:R.193, B:R.193 pi-Stacking: B:Y.186

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: R.215, R.238, S.240, A.265, A.266, G.329, L.330 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.215, A:A.266 Water bridges: A:G.267, A:G.267 GOL.6: 6 residues within 4Å: Chain A: L.305, G.306, G.307, I.351, D.352, E.357 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.357 Water bridges: A:G.307 GOL.7: 5 residues within 4Å: Chain A: L.242, R.263, V.325, G.329, W.336 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.263 GOL.14: 7 residues within 4Å: Chain B: L.305, G.306, G.307, I.351, D.352, G.354, E.357 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.352, B:E.357 GOL.15: 6 residues within 4Å: Chain B: R.215, R.238, S.239, A.265, A.266, G.329 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.215, B:R.238, B:A.266, B:G.329 Water bridges: B:G.267, B:G.267 GOL.16: 6 residues within 4Å: Chain B: A.128, A.129, A.349, A.350, T.353, A.355 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.128, B:T.353

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.8: 6 residues within 4Å: Chain A: T.70, P.199, T.200, V.201, F.223, L.226 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.223 DMS.9: 3 residues within 4Å: Chain A: G.110, G.112, S.142 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.112, A:S.142 DMS.17: 7 residues within 4Å: Chain B: T.70, P.199, T.200, V.201, L.204, F.223, L.226 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:F.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Evans, G.L. et al., Repurposing the Chemical Scaffold of the Anti-Arthritic Drug Lobenzarit to Target Tryptophan Biosynthesis in Mycobacterium tuberculosis. Chembiochem (2014)

Release Date

2013-08-14

Peptides

Anthranilate phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Anthranilate phosphoribosyltransferase

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