SMTL ID : 3nv8.1

The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase in complex with phosphoenol pyruvate and manganese (thesit-free)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: T.41, D.140, R.147, R.150, H.166 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.148 Water bridges: A:R.147, A:H.166 Salt bridges: A:R.147, A:R.150, A:H.166 SO4.6: 5 residues within 4Å: Chain B: R.25, L.28, R.51, 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 SO4.7: 4 residues within 4Å: Chain B: R.137, S.138, A.139, R.286 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.138, B:S.138, B:A.139 Salt bridges: B:R.137, B:R.286 SO4.15: 5 residues within 4Å: Chain C: T.41, D.140, R.147, R.150, H.166 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.148 Water bridges: C:R.147, C:H.166 Salt bridges: C:R.147, C:R.150, C:H.166 SO4.20: 5 residues within 4Å: Chain D: R.25, L.28, R.51, 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 SO4.21: 4 residues within 4Å: Chain D: R.137, S.138, A.139, R.286 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.138, D:S.138, D:A.139 Salt bridges: D:R.137, D:R.286

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

MN.2: 5 residues within 4Å: Chain A: C.89, H.371, E.413, D.443 Ligands: PEP.5 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.8: 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.16: 5 residues within 4Å: Chain C: C.89, H.371, E.413, D.443 Ligands: PEP.19 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.22: 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

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: R.170, R.173 Chain B: P.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.170, A:R.170, A:R.173, A:R.173 Water bridges: A:F.157 GOL.4: 5 residues within 4Å: Chain A: R.173, A.176, N.177 Chain B: I.9, V.57 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.173, A:N.177 GOL.9: 5 residues within 4Å: Chain B: L.109, T.116, V.123, K.125, L.196 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.116, B:V.123, B:V.123 Water bridges: B:E.244 GOL.10: 7 residues within 4Å: Chain B: Q.72, V.123, V.124, K.125, Q.241, E.244, Y.246 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.72, B:K.125, B:K.125, B:Q.241 Water bridges: B:E.244 GOL.11: 3 residues within 4Å: Chain B: P.19, L.20, R.25 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.20, B:R.25, B:R.25 GOL.12: 5 residues within 4Å: Chain B: R.27, A.31, A.296, Q.299, V.300 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.27, B:R.27, B:A.296, B:Q.299 GOL.17: 3 residues within 4Å: Chain C: R.170, R.173 Chain D: P.10 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.170, C:R.170, C:R.173, C:R.173 Water bridges: C:F.157 GOL.18: 5 residues within 4Å: Chain C: R.173, A.176, N.177 Chain D: I.9, V.57 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.173, C:N.177 GOL.23: 5 residues within 4Å: Chain D: L.109, T.116, V.123, K.125, L.196 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.116, D:T.116, D:V.123, D:V.123 Water bridges: D:E.244 GOL.24: 7 residues within 4Å: Chain D: Q.72, V.123, V.124, K.125, Q.241, E.244, Y.246 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Q.72, D:K.125, D:K.125, D:Q.241, D:E.244 Water bridges: D:E.244 GOL.25: 3 residues within 4Å: Chain D: P.19, L.20, R.25 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.20, D:R.25, D:R.25 GOL.26: 5 residues within 4Å: Chain D: R.27, A.31, A.296, Q.299, V.300 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.27, D:R.27, D:A.296, D:Q.299

2 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.5: 10 residues within 4Å: Chain A: R.128, E.250, W.282, G.284, E.285, K.308, R.339, H.371, E.413 Ligands: MN.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.285 Salt bridges: A:R.128, A:K.308, A:K.308, A:R.339, A:H.371, A:H.371, A:H.411 PEP.19: 10 residues within 4Å: Chain C: R.128, E.250, W.282, G.284, E.285, K.308, R.339, H.371, E.413 Ligands: MN.16 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:E.285 Salt bridges: C:R.128, C:K.308, C:K.308, C:R.339, C:H.371, C:H.371, C:H.411

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

CL.13: 2 residues within 4Å: Chain B: R.51, R.258 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain D: R.51, R.258 Ligand excluded by PLIP

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

PO4.14: 5 residues within 4Å: Chain B: G.284, E.285, K.308, R.339, H.371 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.285 Salt bridges: B:K.308, B:R.339, B:H.371 PO4.28: 5 residues within 4Å: Chain D: G.284, E.285, K.308, R.339, H.371 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.285 Salt bridges: D:K.308, D:R.339, D:H.371

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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