SMTL ID : 3nud.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

10 x PHE: PHENYLALANINE(Non-covalent)

PHE.1: 6 residues within 4Å: Chain A: F.93, R.173, A.176, N.177 Chain B: V.7, V.57 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.176 Hydrogen bonds: A:F.93, A:N.177 Salt bridges: A:R.173 PHE.3: 10 residues within 4Å: Chain A: L.109, V.113, K.125, A.194, N.239, L.240, Q.241, T.242, A.243 Chain C: C.233 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.109, A:V.113, A:A.243 Hydrogen bonds: A:Q.241, A:T.242, C:C.233 Salt bridges: A:K.125 PHE.5: 7 residues within 4Å: Chain A: I.11, V.57, Y.175 Chain B: F.93, R.173, A.176, N.177 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.176, A:Y.175 Hydrogen bonds: B:F.93, B:N.177 PHE.6: 10 residues within 4Å: Chain B: L.109, V.113, K.125, A.194, L.196, N.239, L.240, Q.241, A.243 Chain D: C.233 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:L.109, B:V.113, B:L.196, B:A.243 Hydrogen bonds: B:N.239, D:C.233 Salt bridges: B:K.125 pi-Cation interactions: B:K.125 PHE.7: 7 residues within 4Å: Chain B: L.20, R.25, L.28, E.55, R.258, L.261 Ligands: PO4.10 9 PLIP interactions: 7 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:L.20, B:L.20, B:L.28, B:L.261 Hydrogen bonds: B:E.55, F.7, F.7 Salt bridges: B:R.25, B:R.258 PHE.11: 6 residues within 4Å: Chain C: F.93, R.173, A.176, N.177 Chain D: V.7, V.57 4 PLIP interactions: 4 interactions with chain C, Hydrophobic interactions: C:A.176 Hydrogen bonds: C:F.93, C:N.177 Salt bridges: C:R.173 PHE.13: 10 residues within 4Å: Chain A: C.233 Chain C: L.109, V.113, K.125, A.194, N.239, L.240, Q.241, T.242, A.243 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.109, C:V.113, C:A.243 Hydrogen bonds: C:Q.241, C:T.242, A:C.233 Salt bridges: C:K.125 PHE.15: 7 residues within 4Å: Chain C: I.11, V.57, Y.175 Chain D: F.93, R.173, A.176, N.177 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C, Hydrophobic interactions: D:A.176, C:Y.175 Hydrogen bonds: D:F.93, D:N.177 PHE.16: 10 residues within 4Å: Chain B: C.233 Chain D: L.109, V.113, K.125, A.194, L.196, N.239, L.240, Q.241, A.243 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain D, Hydrogen bonds: B:C.233 Hydrophobic interactions: D:L.109, D:V.113, D:L.196, D:A.243 Salt bridges: D:K.125 pi-Cation interactions: D:K.125 PHE.17: 7 residues within 4Å: Chain D: L.20, R.25, L.28, E.55, R.258, L.261 Ligands: PO4.20 10 PLIP interactions: 8 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:L.20, D:L.20, D:L.28, D:L.261 Hydrogen bonds: D:E.55, D:E.55, F.17, F.17 Salt bridges: D:R.25, D:R.258

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

PO4.2: 6 residues within 4Å: Chain A: G.284, E.285, R.286, K.308, R.339, H.371 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.285, A:R.286 Salt bridges: A:K.308, A:R.339, A:H.371 PO4.4: 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 Salt bridges: A:R.137, A:R.286 PO4.8: 5 residues within 4Å: Chain B: G.284, E.285, K.308, R.339, H.371 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.285, B:R.286 Salt bridges: B:K.308, B:R.339, B:H.371 PO4.9: 4 residues within 4Å: Chain B: R.137, S.138, A.139, R.286 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.138, B:A.139 Salt bridges: B:R.137, B:R.286 PO4.10: 4 residues within 4Å: Chain B: P.19, L.20, R.25 Ligands: PHE.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.20 Salt bridges: B:R.25 PO4.12: 6 residues within 4Å: Chain C: G.284, E.285, R.286, K.308, R.339, H.371 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.285, C:R.286 Salt bridges: C:K.308, C:R.339, C:H.371 PO4.14: 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 Salt bridges: C:R.137, C:R.286 PO4.18: 5 residues within 4Å: Chain D: G.284, E.285, K.308, R.339, H.371 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.285, D:R.286 Salt bridges: D:K.308, D:R.339, D:H.371 PO4.19: 4 residues within 4Å: Chain D: R.137, S.138, A.139, R.286 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.138, D:A.139 Salt bridges: D:R.137, D:R.286 PO4.20: 4 residues within 4Å: Chain D: P.19, L.20, R.25 Ligands: PHE.17 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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