SMTL ID : 3pfp.1

Structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis in complex with an active site inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 6 residues within 4Å: Chain A: C.89, H.371, E.413, D.443 Ligands: 035.2, 036.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.89, A:H.371, A:E.413, A:E.413, A:D.443 MN.4: 6 residues within 4Å: Chain B: C.89, H.371, E.413, D.443 Ligands: 036.5, 035.8 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:C.89, B:H.371, B:E.413, B:E.413, B:D.443 MN.9: 6 residues within 4Å: Chain C: C.89, H.371, E.413, D.443 Ligands: 035.10, 036.11 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:C.89, C:H.371, C:E.413, C:E.413, C:D.443 MN.12: 6 residues within 4Å: Chain D: C.89, H.371, E.413, D.443 Ligands: 036.13, 035.16 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:C.89, D:H.371, D:E.413, D:E.413, D:D.443

4 x 035: (2S)-2,7-bis(phosphonooxy)heptanoic acid(Non-covalent)

035.2: 19 residues within 4Å: Chain A: C.89, R.128, K.135, P.136, R.137, S.138, W.282, G.284, E.285, R.286, K.308, R.339, H.371, K.382, E.413, C.442, D.443 Ligands: MN.1, 036.3 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:P.136 Hydrogen bonds: A:S.138, A:S.138, A:E.285 Water bridges: A:R.137, A:S.138, A:A.139, A:E.250, A:R.286, A:R.286, A:R.286, A:K.382 Salt bridges: A:R.128, A:K.135, A:R.137, A:R.286, A:R.286, A:K.308, A:K.308, A:R.339, A:H.371, A:H.371, A:K.382 035.8: 19 residues within 4Å: Chain B: C.89, R.128, K.135, P.136, R.137, S.138, W.282, G.284, E.285, R.286, K.308, R.339, H.371, K.382, E.413, C.442, D.443 Ligands: MN.4, 036.5 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:P.136 Hydrogen bonds: B:S.138, B:E.285 Water bridges: B:R.137, B:R.137, B:S.138, B:A.139, B:A.139, B:R.286, B:R.286, B:R.286, B:K.308, B:H.371 Salt bridges: B:R.128, B:K.135, B:R.137, B:R.286, B:R.286, B:K.308, B:K.308, B:R.339, B:H.371, B:H.371, B:K.382 035.10: 19 residues within 4Å: Chain C: C.89, R.128, K.135, P.136, R.137, S.138, W.282, G.284, E.285, R.286, K.308, R.339, H.371, K.382, E.413, C.442, D.443 Ligands: MN.9, 036.11 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:P.136 Hydrogen bonds: C:S.138, C:S.138, C:E.285 Water bridges: C:R.137, C:S.138, C:A.139, C:E.250, C:R.286, C:R.286, C:R.286, C:K.382 Salt bridges: C:R.128, C:K.135, C:R.137, C:R.286, C:R.286, C:K.308, C:K.308, C:R.339, C:H.371, C:H.371, C:K.382 035.16: 19 residues within 4Å: Chain D: C.89, R.128, K.135, P.136, R.137, S.138, W.282, G.284, E.285, R.286, K.308, R.339, H.371, K.382, E.413, C.442, D.443 Ligands: MN.12, 036.13 28 PLIP interactions: 28 interactions with chain D Hydrophobic interactions: D:P.136 Hydrogen bonds: D:S.138, D:S.138, D:S.138, D:E.285, D:D.443, D:D.443 Water bridges: D:R.137, D:R.137, D:S.138, D:A.139, D:A.139, D:R.286, D:R.286, D:R.286, D:K.308, D:H.371 Salt bridges: D:R.128, D:K.135, D:R.137, D:R.286, D:R.286, D:K.308, D:K.308, D:R.339, D:H.371, D:H.371, D:K.382

4 x 036: (2R)-2,7-bis(phosphonooxy)heptanoic acid(Non-covalent)

036.3: 17 residues within 4Å: Chain A: C.89, R.128, K.135, P.136, R.137, S.138, G.284, E.285, R.286, K.308, R.339, H.371, K.382, E.413, D.443 Ligands: MN.1, 035.2 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:S.138, A:E.285 Water bridges: A:A.139, A:E.250, A:W.282, A:R.286, A:R.339, A:K.382, A:K.382 Salt bridges: A:R.128, A:K.135, A:R.137, A:R.286, A:K.308, A:K.308, A:R.339, A:H.371, A:H.371, A:K.382 036.5: 20 residues within 4Å: Chain B: C.89, R.128, K.135, P.136, R.137, S.138, E.250, W.282, G.284, E.285, R.286, K.308, R.339, H.371, K.382, E.413, C.442, D.443 Ligands: MN.4, 035.8 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:P.136 Hydrogen bonds: B:S.138, B:W.282, B:E.285 Water bridges: B:R.137, B:R.137, B:S.138, B:S.138, B:A.139, B:E.250, B:R.286, B:K.308, B:R.339 Salt bridges: B:R.128, B:K.135, B:R.137, B:R.286, B:K.308, B:K.308, B:R.339, B:H.371, B:H.371, B:K.382 036.11: 17 residues within 4Å: Chain C: C.89, R.128, K.135, P.136, R.137, S.138, G.284, E.285, R.286, K.308, R.339, H.371, K.382, E.413, D.443 Ligands: MN.9, 035.10 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:S.138, C:E.285 Water bridges: C:A.139, C:E.250, C:W.282, C:R.286, C:R.339, C:K.382, C:K.382 Salt bridges: C:R.128, C:K.135, C:R.137, C:R.286, C:K.308, C:K.308, C:R.339, C:H.371, C:H.371, C:K.382 036.13: 20 residues within 4Å: Chain D: C.89, R.128, K.135, P.136, R.137, S.138, E.250, W.282, G.284, E.285, R.286, K.308, R.339, H.371, K.382, E.413, C.442, D.443 Ligands: MN.12, 035.16 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:P.136 Hydrogen bonds: D:S.138, D:S.138, D:S.138, D:W.282, D:E.285 Water bridges: D:R.137, D:R.137, D:S.138, D:S.138, D:A.139, D:E.250, D:R.286, D:K.308, D:R.339 Salt bridges: D:R.128, D:K.135, D:R.137, D:R.286, D:K.308, D:K.308, D:R.339, D:H.371, D:H.371, D:K.382

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 2 residues within 4Å: Chain B: N.418, R.437 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain D: N.418, R.437 Ligand excluded by PLIP

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 4 residues within 4Å: Chain B: R.25, L.28, E.55, R.258 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.51, B:R.258 Salt bridges: B:R.25, B:R.258 SO4.15: 4 residues within 4Å: Chain D: R.25, L.28, E.55, R.258 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.51, D:E.55, D:R.258 Salt bridges: D:R.25, D:R.258

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reichau, S. et al., Potent inhibitors of a shikimate pathway enzyme from Mycobacterium tuberculosis: combining mechanism- and modeling-based design. J.Biol.Chem. (2011)

Release Date

2011-03-16

Peptides

Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG

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