SMTL ID : 3kgf.1

The structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis complexed with phenylalanine and tryptophan

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

6 x PHE: PHENYLALANINE(Non-covalent)

PHE.1: 11 residues within 4Å: Chain A: F.93, M.94, R.173, A.176, N.177, A.180 Chain B: W.5, V.7, D.8, V.57, Y.175 11 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:A.176, A:A.180, B:W.5, B:V.57, B:Y.175 Hydrogen bonds: A:F.93, A:N.177, A:N.177, B:D.8, F.1 Salt bridges: A:R.173 PHE.17: 7 residues within 4Å: Chain A: V.57, Y.175 Chain B: F.93, R.173, A.176, N.177, A.180 10 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:A.176, B:A.180, A:V.57, A:Y.175 Hydrogen bonds: B:F.93, B:N.177 Water bridges: B:R.173, A:D.12, F.17 Salt bridges: B:R.173 PHE.25: 7 residues within 4Å: Chain B: L.20, R.25, L.28, E.55, R.258, L.261, L.273 10 PLIP interactions: 9 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:L.20, B:L.20, B:L.28, B:L.261, B:L.273 Hydrogen bonds: B:E.55 Water bridges: B:E.55, F.25 Salt bridges: B:R.25, B:R.258 PHE.31: 11 residues within 4Å: Chain C: F.93, M.94, R.173, A.176, N.177, A.180 Chain D: W.5, V.7, D.8, V.57, Y.175 11 PLIP interactions: 1 Ligand-Ligand interactions, 6 interactions with chain C, 4 interactions with chain D Hydrogen bonds: F.31, C:F.93, C:N.177, C:N.177, D:D.8 Hydrophobic interactions: C:A.176, C:A.180, D:W.5, D:V.57, D:Y.175 Salt bridges: C:R.173 PHE.47: 7 residues within 4Å: Chain C: V.57, Y.175 Chain D: F.93, R.173, A.176, N.177, A.180 10 PLIP interactions: 3 interactions with chain C, 6 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: C:V.57, C:Y.175, D:A.176, D:A.180 Water bridges: C:D.12, D:R.173, F.47 Hydrogen bonds: D:F.93, D:N.177 Salt bridges: D:R.173 PHE.55: 7 residues within 4Å: Chain D: L.20, R.25, L.28, E.55, R.258, L.261, L.273 11 PLIP interactions: 10 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:L.20, D:L.20, D:L.28, D:L.261, D:L.273 Hydrogen bonds: D:E.55, D:E.55 Water bridges: D:E.55, F.55 Salt bridges: D:R.25, D:R.258

4 x TRP: TRYPTOPHAN(Non-covalent)

TRP.2: 12 residues within 4Å: Chain A: L.109, A.112, V.113, K.125, A.194, L.196, N.239, L.240, T.242, A.243 Chain C: A.232, C.233 15 PLIP interactions: 10 interactions with chain A, 5 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, A:E.244, W.2, W.2, W.2 Salt bridges: A:K.125 TRP.18: 12 residues within 4Å: Chain B: L.109, A.112, V.113, T.116, K.125, A.194, L.196, N.239, L.240, T.242, A.243 Chain D: C.233 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:L.109, B:A.112, 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 Salt bridges: B:K.125 TRP.32: 12 residues within 4Å: Chain A: A.232, C.233 Chain C: L.109, A.112, V.113, K.125, A.194, L.196, N.239, L.240, T.242, A.243 15 PLIP interactions: 10 interactions with chain C, 5 Ligand-Ligand interactions Hydrophobic interactions: C:L.109, C:V.113, C:L.196 Hydrogen bonds: C:A.194, C:N.239, W.32, W.32 Water bridges: C:K.125, C:N.239, C:N.239, C:E.244, W.32, W.32, W.32 Salt bridges: C:K.125 TRP.48: 12 residues within 4Å: Chain B: C.233 Chain D: L.109, A.112, V.113, T.116, K.125, A.194, L.196, N.239, L.240, T.242, A.243 12 PLIP interactions: 12 interactions with chain D, Hydrophobic interactions: D:L.109, D:A.112, 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 Salt bridges: D:K.125

32 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: T.26, D.29, A.30 Ligands: GOL.11 Ligand excluded by PLIP GOL.4: 8 residues within 4Å: Chain A: L.32, K.34, A.36, Q.39, L.254, D.255, R.258, A.293 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: Q.46, M.50, D.167, S.169 Chain B: M.3, N.4 Ligand excluded by PLIP GOL.10: 9 residues within 4Å: Chain A: E.65, M.182, R.186, T.189, A.243, E.244, I.245, Y.246, H.279 Ligand excluded by PLIP GOL.11: 4 residues within 4Å: Chain A: R.25, T.26, D.29 Ligands: GOL.3 Ligand excluded by PLIP GOL.13: 6 residues within 4Å: Chain A: S.190, S.191, G.192, S.195, Q.241, T.242 Ligand excluded by PLIP GOL.14: 3 residues within 4Å: Chain A: L.48, A.49, T.52 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain A: R.137, S.138, A.139, R.286 Ligand excluded by PLIP GOL.16: 8 residues within 4Å: Chain A: Q.38, R.137, S.138, A.139, D.140, R.150 Ligands: PO4.6, CL.8 Ligand excluded by PLIP GOL.23: 6 residues within 4Å: Chain B: Q.72, P.122, V.123, V.124, K.125, E.244 Ligand excluded by PLIP GOL.24: 10 residues within 4Å: Chain B: E.65, R.68, M.182, R.186, T.189, A.243, E.244, I.245, Y.246, H.279 Ligand excluded by PLIP GOL.26: 6 residues within 4Å: Chain B: L.32, A.36, Q.39, L.254, D.255, R.258 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain B: T.92, M.94, D.95, F.157, E.439 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain B: I.9, D.45, L.48, A.49, T.52 Ligand excluded by PLIP GOL.29: 7 residues within 4Å: Chain A: S.64, D.265 Chain B: R.102, S.191, G.192, L.193, L.198 Ligand excluded by PLIP GOL.30: 3 residues within 4Å: Chain B: P.35, A.36, A.37 Ligand excluded by PLIP GOL.33: 4 residues within 4Å: Chain C: T.26, D.29, A.30 Ligands: GOL.41 Ligand excluded by PLIP GOL.34: 8 residues within 4Å: Chain C: L.32, K.34, A.36, Q.39, L.254, D.255, R.258, A.293 Ligand excluded by PLIP GOL.39: 6 residues within 4Å: Chain C: Q.46, M.50, D.167, S.169 Chain D: M.3, N.4 Ligand excluded by PLIP GOL.40: 9 residues within 4Å: Chain C: E.65, M.182, R.186, T.189, A.243, E.244, I.245, Y.246, H.279 Ligand excluded by PLIP GOL.41: 4 residues within 4Å: Chain C: R.25, T.26, D.29 Ligands: GOL.33 Ligand excluded by PLIP GOL.43: 6 residues within 4Å: Chain C: S.190, S.191, G.192, S.195, Q.241, T.242 Ligand excluded by PLIP GOL.44: 3 residues within 4Å: Chain C: L.48, A.49, T.52 Ligand excluded by PLIP GOL.45: 4 residues within 4Å: Chain C: R.137, S.138, A.139, R.286 Ligand excluded by PLIP GOL.46: 8 residues within 4Å: Chain C: Q.38, R.137, S.138, A.139, D.140, R.150 Ligands: PO4.36, CL.38 Ligand excluded by PLIP GOL.53: 6 residues within 4Å: Chain D: Q.72, P.122, V.123, V.124, K.125, E.244 Ligand excluded by PLIP GOL.54: 10 residues within 4Å: Chain D: E.65, R.68, M.182, R.186, T.189, A.243, E.244, I.245, Y.246, H.279 Ligand excluded by PLIP GOL.56: 6 residues within 4Å: Chain D: L.32, A.36, Q.39, L.254, D.255, R.258 Ligand excluded by PLIP GOL.57: 5 residues within 4Å: Chain D: T.92, M.94, D.95, F.157, E.439 Ligand excluded by PLIP GOL.58: 5 residues within 4Å: Chain D: I.9, D.45, L.48, A.49, T.52 Ligand excluded by PLIP GOL.59: 7 residues within 4Å: Chain C: S.64, D.265 Chain D: R.102, S.191, G.192, L.193, L.198 Ligand excluded by PLIP GOL.60: 3 residues within 4Å: Chain D: P.35, A.36, A.37 Ligand excluded by PLIP

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

PO4.5: 5 residues within 4Å: Chain A: G.284, E.285, K.308, R.339, H.371 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:E.285 Water bridges: A:E.250, A:W.282, A:R.286, A:R.286, A:R.286, A:R.286, A:K.308, A:K.308 Salt bridges: A:K.308, A:R.339, A:H.371 PO4.6: 5 residues within 4Å: Chain A: T.41, R.147, R.150, H.166 Ligands: GOL.16 9 PLIP interactions: 9 interactions with chain A Water bridges: A:D.140, A:R.147, A:R.147, A:R.147, A:R.150, A:R.150 Salt bridges: A:R.147, A:R.150, A:H.166 PO4.19: 5 residues within 4Å: Chain B: G.284, E.285, K.308, R.339, H.371 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.285, B:R.286 Water bridges: B:R.286, B:R.286, B:K.308 Salt bridges: B:K.308, B:R.339, B:H.371 PO4.35: 5 residues within 4Å: Chain C: G.284, E.285, K.308, R.339, H.371 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:E.285 Water bridges: C:E.250, C:W.282, C:R.286, C:R.286, C:R.286, C:R.286, C:K.308, C:K.308 Salt bridges: C:K.308, C:R.339, C:H.371 PO4.36: 5 residues within 4Å: Chain C: T.41, R.147, R.150, H.166 Ligands: GOL.46 9 PLIP interactions: 9 interactions with chain C Water bridges: C:D.140, C:R.147, C:R.147, C:R.147, C:R.150, C:R.150 Salt bridges: C:R.147, C:R.150, C:H.166 PO4.49: 5 residues within 4Å: Chain D: G.284, E.285, K.308, R.339, H.371 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:E.285, D:R.286 Water bridges: D:R.286, D:R.286, D:K.308 Salt bridges: D:K.308, D:R.339, D:H.371

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

MN.7: 4 residues within 4Å: Chain A: C.89, H.371, E.413, D.443 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.89, A:H.371, A:E.413, A:D.443, H2O.5 MN.22: 4 residues within 4Å: Chain B: C.89, H.371, E.413, D.443 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.37: 4 residues within 4Å: Chain C: C.89, H.371, E.413, D.443 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.89, C:H.371, C:E.413, C:D.443, H2O.34 MN.52: 4 residues within 4Å: Chain D: C.89, H.371, E.413, D.443 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 CL: CHLORIDE ION(Non-functional Binders)

CL.8: 2 residues within 4Å: Chain A: Q.38 Ligands: GOL.16 Ligand excluded by PLIP CL.12: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.38: 2 residues within 4Å: Chain C: Q.38 Ligands: GOL.46 Ligand excluded by PLIP CL.42: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

SO4.20: 4 residues within 4Å: Chain B: R.137, S.138, A.139, R.286 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.138, B:A.139 Water bridges: B:R.137, B:S.148 Salt bridges: B:R.137, B:R.286 SO4.21: 3 residues within 4Å: Chain B: P.19, L.20, R.25 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.20 Salt bridges: B:R.25 SO4.50: 4 residues within 4Å: Chain D: R.137, S.138, A.139, R.286 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.138, D:A.139 Water bridges: D:R.137, D:S.148 Salt bridges: D:R.137, D:R.286 SO4.51: 3 residues within 4Å: Chain D: P.19, L.20, R.25 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.20 Salt bridges: D:R.25

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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