SMTL ID : 3r88.1

Anthranilate phosphoribosyltransferase (trpD) from Mycobacterium tuberculosis (complex with inhibitor ACS145)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 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, H.135, N.137, A.139, A.140, S.141, S.142, G.145, G.146, E.251 Ligands: MG.2, MG.3 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:G.106, A:G.109, A:N.116, A:S.118, 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:L.117, A:L.117, A:K.134, A:H.135, A:A.147, A:R.192 Salt bridges: A:K.134, A:K.134 PRP.5: 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.6, MG.7 25 PLIP interactions: 25 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:G.146 Water bridges: B:G.106, B:D.110, B:T.114, B:T.114, B:K.134, B:K.134, B:H.135, B:S.142, B:E.251, B:E.251, B:E.251 Salt bridges: B:K.134

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: G.106, S.118, 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.11, H2O.11 MG.3: 5 residues within 4Å: Chain A: D.110, D.250, E.251 Ligands: PRP.1, MG.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.250, H2O.5, H2O.11, H2O.11, H2O.11 MG.6: 4 residues within 4Å: Chain B: D.250, E.251 Ligands: PRP.5, MG.7 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.250, B:E.251, H2O.15, H2O.18, H2O.24 MG.7: 5 residues within 4Å: Chain B: G.106, S.118, E.251 Ligands: PRP.5, MG.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.118, B:E.251, H2O.14, H2O.15

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x 14F: 2-amino-4,5-dimethoxybenzoic acid(Non-covalent)

14F.8: 9 residues within 4Å: Chain B: N.137, A.178, P.179, H.182, P.183, Y.185, R.186, A.189, R.193 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:P.179, B:P.179, B:Y.185, B:A.189 Hydrogen bonds: B:N.137, B:H.182 Water bridges: B:R.193, B:R.193 Salt bridges: B:R.193

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
A

B
B

Anthranilate phosphoribosyltransferase

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