SMTL ID : 4n5v.1

Alternative substrates of Mycobacterium tuberculosis anthranilate phosphoribosyl transferase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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, FA0.4 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:G.107, A:G.110, A:N.117, A:L.118, A:S.119, A:S.119, 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:D.111, A:D.111, A:K.135, A:A.148, A:R.193, A:R.193, A:E.252, A:E.252 Salt bridges: A:K.135 PRP.8: 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.9, MG.10, FA0.12 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: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:G.112, B:L.118, B:L.118, B:K.135, B:A.148, B:D.251 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.1 MG.3: 5 residues within 4Å: Chain A: D.111, D.251, E.252 Ligands: PRP.1, MG.2 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.251, A:E.252, H2O.1, H2O.9, H2O.10 MG.9: 6 residues within 4Å: Chain B: G.107, S.119, D.251, E.252 Ligands: PRP.8, MG.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.119, B:E.252, H2O.12, H2O.12 MG.10: 5 residues within 4Å: Chain B: D.111, D.251, E.252 Ligands: PRP.8, MG.9 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.251, B:E.252, H2O.12, H2O.13, H2O.18

4 x FA0: 2-amino-4-fluorobenzoic acid(Non-covalent)

FA0.4: 12 residues within 4Å: Chain A: V.106, G.107, T.108, H.136, G.137, N.138, A.179, R.193, G.206, P.207 Ligands: PRP.1, FA0.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.106, A:N.138, A:A.179 Hydrogen bonds: A:G.107, A:N.138 Water bridges: A:R.193, A:R.193, A:R.193, A:R.193, A:R.193, A:N.203 Salt bridges: A:R.193 FA0.5: 10 residues within 4Å: Chain A: N.138, A.179, P.180, H.183, P.184, Y.186, R.187, A.190, R.194 Ligands: FA0.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.180, A:H.183, A:A.190 Hydrogen bonds: A:H.183 Water bridges: A:A.191, A:R.194, A:R.194 Salt bridges: A:R.194 FA0.11: 9 residues within 4Å: Chain B: N.138, A.179, P.180, H.183, Y.186, R.187, A.190, R.194 Ligands: FA0.12 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:H.183, B:A.190 Hydrogen bonds: B:H.183 Water bridges: B:R.194, B:R.194, B:R.194 Salt bridges: B:R.194 FA0.12: 12 residues within 4Å: Chain B: V.106, G.107, T.108, H.136, G.137, N.138, A.179, R.193, G.206, P.207 Ligands: PRP.8, FA0.11 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.106, B:N.138, B:A.179 Hydrogen bonds: B:G.107, B:N.138 Water bridges: B:R.193, B:R.193 Salt bridges: B:R.193 pi-Stacking: B:H.136

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: F.274, D.275, G.278, W.336 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.275, A:G.278, A:W.336 GOL.7: 3 residues within 4Å: Chain A: R.194, E.195 Chain B: P.28 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:R.194, B:W.27 GOL.13: 6 residues within 4Å: Chain B: T.273, F.274, D.275, G.278, F.279, W.336 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.275, B:G.278, B:W.336

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cookson, T.V. et al., Alternative substrates reveal catalytic cycle and key binding events in the reaction catalysed by anthranilate phosphoribosyltransferase from Mycobacterium tuberculosis. Biochem.J. (2014)

Release Date

2014-04-23

Peptides

Anthranilate phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Anthranilate phosphoribosyltransferase

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