SMTL ID : 4gkm.1

Bianthranilate-like analogue bound in the outer 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.107, G.108, G.110, G.111, N.118, L.119, S.120, T.121, K.136, H.137, N.139, A.141, A.142, S.143, S.144, G.147, G.148, E.253 Ligands: MG.2, MG.3, GOL.7 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:T.121, A:N.139, A:A.142, A:S.143, A:S.144, A:S.144, A:G.148 Water bridges: A:D.112, A:G.113, A:L.119, A:L.119, A:N.139, A:N.139 Salt bridges: A:K.136, A:K.136 PRP.9: 20 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, A.141, A.142, S.143, S.144, G.147, G.148, E.253 Ligands: MG.10, MG.11, GOL.15 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:G.108, B:G.111, B:N.118, B:S.120, B:S.120, B:T.121, B:T.121, B:T.121, B:N.139, B:N.139, B:A.142, B:S.143, B:S.144, B:S.144, B:S.144, B:G.148 Water bridges: B:D.112, B:N.115, B:N.115, B:L.119, B:L.119, B:K.136, B:K.136 Salt bridges: B:K.136, B:K.136

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: G.108, S.120, D.252, E.253 Ligands: PRP.1, MG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.120, A:E.253, H2O.7, H2O.7 MG.3: 5 residues within 4Å: Chain A: D.112, D.252, E.253 Ligands: PRP.1, MG.2 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.252, A:E.253, H2O.7, H2O.7, H2O.7, H2O.7 MG.10: 6 residues within 4Å: Chain B: G.108, S.120, D.252, E.253 Ligands: PRP.9, MG.11 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.120, B:E.253, H2O.17, H2O.17 MG.11: 5 residues within 4Å: Chain B: D.112, D.252, E.253 Ligands: PRP.9, MG.10 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.252, B:E.253, H2O.17, H2O.17, H2O.17, H2O.17

2 x 683: 2-[(2-carboxyphenyl)amino]-5-methylbenzoic acid(Non-covalent)

683.4: 14 residues within 4Å: Chain A: M.87, N.139, A.180, P.181, H.184, P.185, Y.187, R.188, A.191, R.194, R.195, G.207, T.210 Ligands: GOL.7 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.180, A:P.181, A:Y.187, A:Y.187, A:R.188 Hydrogen bonds: A:N.139 Water bridges: A:Y.187, A:R.194 Salt bridges: A:R.194, A:R.195, A:R.195 683.12: 14 residues within 4Å: Chain B: M.87, N.139, A.180, P.181, H.184, P.185, Y.187, R.188, A.191, R.194, R.195, G.207, T.210 Ligands: GOL.15 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:A.180, B:P.181, B:Y.187, B:Y.187, B:R.188 Hydrogen bonds: B:N.139 Water bridges: B:R.194, B:R.195, B:R.195 Salt bridges: B:R.194, B:R.195, B:R.195

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: R.264, V.326, G.330, A.335, W.337 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.264, A:V.326 Water bridges: A:V.265 GOL.6: 4 residues within 4Å: Chain A: G.44, A.47, W.48, D.51 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.44, A:D.51 GOL.7: 9 residues within 4Å: Chain A: V.107, G.108, H.137, G.138, N.139, G.207, P.208 Ligands: PRP.1, 683.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.137, A:N.139, A:G.207 Water bridges: A:G.207 GOL.13: 8 residues within 4Å: Chain B: R.264, A.266, V.326, A.329, G.330, A.335, W.337, A.340 2 PLIP interactions: 2 interactions with chain B Water bridges: B:V.242, B:V.265 GOL.14: 4 residues within 4Å: Chain B: G.44, A.47, W.48, D.51 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.44, B:A.47 GOL.15: 9 residues within 4Å: Chain B: V.107, G.108, H.137, G.138, N.139, G.207, P.208 Ligands: PRP.9, 683.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.108, B:H.137, B:N.139 Water bridges: B:G.207 GOL.16: 6 residues within 4Å: Chain B: L.306, G.307, G.308, I.352, G.355, E.358 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.358 Water bridges: B:G.308, B:E.358

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

DMS.8: 6 residues within 4Å: Chain A: R.216, R.239, A.266, A.267, G.330, L.331 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.267 Water bridges: A:G.268 DMS.17: 6 residues within 4Å: Chain B: R.216, R.239, A.266, A.267, G.330, L.331 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.216 DMS.18: 6 residues within 4Å: Chain B: V.99, P.100, A.213, R.214, P.215, R.216 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.216 Water bridges: B:A.103

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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