SMTL ID : 3nue.1

The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis complexed with tryptophan

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: C.89, H.371, E.413, D.443 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.12: 4 residues within 4Å: Chain B: C.89, H.371, E.413, D.443 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.371, B:E.413, B:D.443 MN.20: 4 residues within 4Å: Chain C: C.89, H.371, E.413, D.443 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.31: 4 residues within 4Å: Chain D: C.89, H.371, E.413, D.443 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.371, D:E.413, D:D.443

4 x TRP: TRYPTOPHAN(Non-covalent)

TRP.2: 11 residues within 4Å: Chain A: L.109, V.113, K.125, A.194, L.196, N.239, L.240, T.242, A.243 Chain C: C.233 Ligands: GOL.6 11 PLIP interactions: 9 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:L.109, A:V.113, A:L.196 Hydrogen bonds: A:A.194, A:N.239, W.2, W.2 Water bridges: A:T.116, A:N.239, A:N.239 Salt bridges: A:K.125 TRP.13: 10 residues within 4Å: Chain B: L.109, V.113, K.125, A.194, L.196, N.239, L.240, T.242, A.243 Chain D: C.233 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:L.109, B:V.113, B:L.196 Hydrogen bonds: B:A.194, B:N.239 Water bridges: B:K.125, B:K.125, B:K.125, B:N.239, B:N.239, D:A.232, D:C.233 Salt bridges: B:K.125 TRP.21: 11 residues within 4Å: Chain A: C.233 Chain C: L.109, V.113, K.125, A.194, L.196, N.239, L.240, T.242, A.243 Ligands: GOL.25 11 PLIP interactions: 9 interactions with chain C, 2 Ligand-Ligand interactions Hydrophobic interactions: C:L.109, C:V.113, C:L.196 Hydrogen bonds: C:A.194, C:N.239, W.21, W.21 Water bridges: C:K.125, C:N.239, C:N.239 Salt bridges: C:K.125 TRP.32: 10 residues within 4Å: Chain B: C.233 Chain D: L.109, V.113, K.125, A.194, L.196, N.239, L.240, T.242, A.243 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain B, Hydrophobic interactions: D:L.109, D:V.113, D:L.196 Hydrogen bonds: D:A.194, D:N.239 Water bridges: D:K.125, D:K.125, D:K.125, D:N.239, D:N.239, B:A.232, B:C.233 Salt bridges: D:K.125

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 5 residues within 4Å: Chain A: G.284, E.285, K.308, R.339, H.371 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.285 Water bridges: A:E.250, A:R.286, A:K.308, A:K.308, A:H.371 Salt bridges: A:K.308, A:R.339, A:H.371 PO4.9: 5 residues within 4Å: Chain B: G.284, E.285, K.308, R.339, H.371 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.285 Water bridges: B:R.286, B:R.286, B:K.308 Salt bridges: B:K.308, B:R.339, B:H.371 PO4.22: 5 residues within 4Å: Chain C: G.284, E.285, K.308, R.339, H.371 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:E.285 Water bridges: C:E.250, C:R.286, C:K.308, C:K.308, C:H.371 Salt bridges: C:K.308, C:R.339, C:H.371 PO4.28: 5 residues within 4Å: Chain D: G.284, E.285, K.308, R.339, H.371 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.285 Water bridges: D:R.286, D:R.286, D:K.308 Salt bridges: D:K.308, D:R.339, D:H.371

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

SO4.4: 4 residues within 4Å: Chain A: D.152, R.170, R.173 Chain B: P.10 4 PLIP interactions: 4 interactions with chain A Water bridges: A:F.93, A:M.94 Salt bridges: A:R.170, A:R.173 SO4.5: 4 residues within 4Å: Chain A: R.137, S.138, A.139, R.286 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.138, A:A.139, A:R.286 Salt bridges: A:R.137 SO4.10: 5 residues within 4Å: Chain B: R.137, S.138, A.139, R.286, K.382 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.138, B:S.138, B:A.139 Salt bridges: B:R.137, B:R.286, B:K.382 SO4.11: 6 residues within 4Å: Chain B: R.25, L.28, R.51, E.55, R.258 Ligands: GOL.18 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.258 Water bridges: B:R.51, B:R.51, B:R.51 Salt bridges: B:R.25, B:R.51, B:R.258 SO4.23: 4 residues within 4Å: Chain C: D.152, R.170, R.173 Chain D: P.10 4 PLIP interactions: 4 interactions with chain C Water bridges: C:F.93, C:M.94 Salt bridges: C:R.170, C:R.173 SO4.24: 4 residues within 4Å: Chain C: R.137, S.138, A.139, R.286 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.138, C:A.139, C:R.286 Salt bridges: C:R.137 SO4.29: 5 residues within 4Å: Chain D: R.137, S.138, A.139, R.286, K.382 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.138, D:S.138, D:A.139 Salt bridges: D:R.137, D:R.286, D:K.382 SO4.30: 6 residues within 4Å: Chain D: R.25, L.28, R.51, E.55, R.258 Ligands: GOL.37 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:E.55, D:R.258 Water bridges: D:R.51, D:R.51, D:R.51 Salt bridges: D:R.25, D:R.51, D:R.258

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: Q.72, P.122, V.123, V.124, K.125, E.244 Ligands: TRP.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:Q.72, A:Q.72, A:E.244 Water bridges: A:K.125, W.2, W.2 GOL.7: 7 residues within 4Å: Chain A: E.65, M.182, R.186, T.189, I.245, Y.246, H.279 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.189, A:I.245 Water bridges: A:T.189, A:E.244, A:Y.246 GOL.14: 6 residues within 4Å: Chain B: Q.72, P.122, V.123, V.124, K.125, E.244 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:Q.72, B:V.123 Water bridges: B:K.125, B:K.125, B:K.125, W.13 GOL.15: 4 residues within 4Å: Chain B: L.24, R.27, Q.272, H.328 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.27, B:Q.272 Water bridges: B:Q.299 GOL.16: 3 residues within 4Å: Chain B: R.27, Q.299, V.300 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.27, B:Q.299, B:Q.299 GOL.18: 8 residues within 4Å: Chain B: L.17, P.18, L.20, R.25, L.261, R.262, L.263 Ligands: SO4.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.25 Water bridges: B:L.263, B:L.263 GOL.19: 9 residues within 4Å: Chain B: R.68, M.182, R.186, T.189, A.243, E.244, I.245, Y.246, H.279 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.68, B:T.189, B:T.189, B:I.245, B:I.245 Water bridges: B:E.65, B:E.65, B:E.244 GOL.25: 7 residues within 4Å: Chain C: Q.72, P.122, V.123, V.124, K.125, E.244 Ligands: TRP.21 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: C:Q.72, C:Q.72 Water bridges: C:K.125, W.21, W.21 GOL.26: 7 residues within 4Å: Chain C: E.65, M.182, R.186, T.189, I.245, Y.246, H.279 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.189, C:T.189, C:I.245 Water bridges: C:E.65, C:E.244, C:Y.246 GOL.33: 6 residues within 4Å: Chain D: Q.72, P.122, V.123, V.124, K.125, E.244 7 PLIP interactions: 6 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: D:Q.72, D:V.123, D:E.244 Water bridges: D:K.125, D:K.125, D:K.125, W.32 GOL.34: 4 residues within 4Å: Chain D: L.24, R.27, Q.272, H.328 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.27, D:Q.272 Water bridges: D:Q.299 GOL.35: 3 residues within 4Å: Chain D: R.27, Q.299, V.300 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.27, D:Q.299, D:Q.299 GOL.37: 8 residues within 4Å: Chain D: L.17, P.18, L.20, R.25, L.261, R.262, L.263 Ligands: SO4.30 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.25 Water bridges: D:L.263, D:L.263 GOL.38: 9 residues within 4Å: Chain D: R.68, M.182, R.186, T.189, A.243, E.244, I.245, Y.246, H.279 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:R.68, D:T.189, D:I.245, D:I.245 Water bridges: D:E.65, D:R.68, D:T.189, D:T.189

2 x CE1: O-DODECANYL OCTAETHYLENE GLYCOL(Non-covalent)

CE1.8: 11 residues within 4Å: Chain A: I.9, F.93, V.172, R.173, Y.175, A.176, N.177 Chain B: I.9, V.57, N.177, A.180 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.9, A:V.172, A:Y.175, A:A.176, B:A.180 Hydrogen bonds: A:R.173, A:R.173, A:N.177 CE1.27: 11 residues within 4Å: Chain C: I.9, F.93, V.172, R.173, Y.175, A.176, N.177 Chain D: I.9, V.57, N.177, A.180 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.9, C:V.172, C:Y.175, C:A.176, D:A.180 Hydrogen bonds: C:R.173, C:R.173, C:N.177

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

CL.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Webby, C.J. et al., Synergistic allostery, a sophisticated regulatory network for the control of aromatic amino acid biosynthesis in Mycobacterium tuberculosis. J.Biol.Chem. (2010)

Release Date

2010-07-28

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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