SMTL ID : 3twp.2 (1 other biounit)

Crystal structure of M. tuberculosis TrpD in complex with an inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-dimer

Ligands

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

PRP.1: 20 residues within 4Å: Chain A: V.105, G.106, G.108, G.109, N.116, L.117, S.118, T.119, K.134, N.137, R.138, A.139, A.140, S.141, S.142, G.145, G.146, E.251 Ligands: MG.2, MG.3 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:G.106, A:G.109, A:N.116, A:S.118, A:S.118, A:T.119, A:N.137, A:N.137, A:A.140, A:S.141, A:S.142, A:S.142, A:G.146 Water bridges: A:G.106, A:T.107, A:D.110, A:G.111, A:T.114, A:L.117, A:S.142, A:S.142, A:A.147, A:A.147, A:R.192, A:R.192 Salt bridges: A:K.134 PRP.6: 20 residues within 4Å: Chain B: V.105, G.106, G.108, G.109, N.116, L.117, S.118, T.119, K.134, N.137, R.138, A.139, A.140, S.141, S.142, G.145, G.146, E.251 Ligands: MG.7, MG.8 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:G.106, B:G.109, B:N.116, B:L.117, B:S.118, B:S.118, B:T.119, B:N.137, B:N.137, B:A.140, B:S.141, B:S.142, B:S.142, B:G.146 Water bridges: B:T.114, B:A.147, B:R.192 Salt bridges: B:K.134

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: G.106, S.118, D.250, E.251 Ligands: PRP.1, MG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.118, A:E.251, H2O.3, H2O.4 MG.3: 5 residues within 4Å: Chain A: D.110, D.250, E.251 Ligands: PRP.1, MG.2 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.250, A:E.251, H2O.4, H2O.10, H2O.12 MG.7: 6 residues within 4Å: Chain B: G.106, S.118, D.250, E.251 Ligands: PRP.6, MG.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.118, B:E.251, H2O.19, H2O.20 MG.8: 5 residues within 4Å: Chain B: D.110, D.250, E.251 Ligands: PRP.6, MG.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.250, B:E.251, H2O.20, H2O.21

2 x SAL: 2-HYDROXYBENZOIC ACID(Non-covalent)

SAL.4: 9 residues within 4Å: Chain A: N.137, A.178, P.179, H.182, P.183, Y.185, R.186, A.189, R.193 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.179, A:P.179, A:R.186, A:A.189 Hydrogen bonds: A:N.137, A:R.193 SAL.9: 8 residues within 4Å: Chain B: N.137, A.178, P.179, H.182, P.183, Y.185, R.186, A.189 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.179 Hydrogen bonds: B:N.137, B:A.178

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: A.140, R.192, R.193, G.196, V.197, P.198, N.202 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.196, A:V.197, A:N.202 Water bridges: A:S.141, A:R.192, A:G.196 GOL.10: 6 residues within 4Å: Chain B: A.140, R.192, G.196, V.197, P.198, N.202 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.192, B:V.197, B:N.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Castell, A. et al., The Substrate Capture Mechanism of Mycobacterium tuberculosis Anthranilate Phosphoribosyltransferase Provides a Mode for Inhibition. Biochemistry (2013)

Release Date

2012-09-26

Peptides

Anthranilate phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Anthranilate phosphoribosyltransferase

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