SMTL ID : 3okf.2 (1 other biounit)

2.5 Angstrom Resolution Crystal Structure of 3-Dehydroquinate Synthase (aroB) from Vibrio cholerae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 27 residues within 4Å: Chain A: N.70, T.72, V.73, L.76, Y.77, D.99, E.101, K.104, G.132, G.133, V.134, D.137, T.157, T.158, L.160, D.164, S.165, K.170, K.179, N.180, C.197, T.200, L.201, P.202, E.205, K.254 Ligands: PO4.4 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:L.160, A:D.164 Hydrogen bonds: A:N.70, A:Y.77, A:D.99, A:E.101, A:G.133, A:V.134, A:D.137, A:T.158, A:K.179, A:K.179, A:N.180, A:K.254 Water bridges: A:D.99, A:K.104, A:K.104, A:G.132, A:G.132, A:T.158, A:E.205 NAD.10: 25 residues within 4Å: Chain B: N.70, T.72, V.73, L.76, Y.77, D.99, E.101, K.104, G.132, G.133, V.134, D.137, T.157, T.158, L.160, D.164, S.165, K.170, K.179, N.180, C.197, T.200, L.201, P.202, E.205 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:L.160, B:D.164 Hydrogen bonds: B:N.70, B:T.72, B:D.99, B:E.101, B:K.104, B:G.133, B:V.134, B:D.137, B:T.157, B:T.158, B:K.179, B:K.179, B:N.180, B:C.197, B:T.200, B:K.254 Water bridges: B:E.101, B:G.132 NAD.15: 27 residues within 4Å: Chain C: N.70, T.72, V.73, L.76, Y.77, D.99, E.101, K.104, G.132, G.133, V.134, D.137, T.157, T.158, L.160, D.164, S.165, K.170, K.179, N.180, C.197, T.200, L.201, P.202, E.205, K.254 Ligands: PO4.18 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:L.160, C:D.164 Hydrogen bonds: C:N.70, C:T.72, C:Y.77, C:Y.77, C:D.99, C:E.101, C:G.133, C:V.134, C:D.137, C:T.157, C:K.179, C:K.179, C:N.180, C:T.200, C:K.254 Water bridges: C:D.99, C:E.101, C:K.104, C:K.104, C:G.132, C:G.132, C:T.158, C:E.205 NAD.24: 25 residues within 4Å: Chain D: N.70, T.72, V.73, L.76, Y.77, D.99, E.101, K.104, G.132, G.133, V.134, D.137, T.157, T.158, L.160, D.164, S.165, K.170, K.179, N.180, C.197, T.200, L.201, P.202, E.205 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:L.160, D:D.164 Hydrogen bonds: D:N.70, D:D.99, D:E.101, D:K.104, D:G.133, D:V.134, D:D.137, D:K.179, D:K.179, D:N.180, D:C.197, D:K.254 Water bridges: D:G.132

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

PO4.2: 3 residues within 4Å: Chain A: K.170, N.180 Chain B: R.148 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.180 Salt bridges: A:K.170, B:R.148 Water bridges: B:R.148 PO4.3: 4 residues within 4Å: Chain A: R.148 Chain B: K.170, N.180 Ligands: PO4.11 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.180 Salt bridges: B:K.170, A:R.148 PO4.4: 5 residues within 4Å: Chain A: K.170, K.254, R.268, L.271 Ligands: NAD.1 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.170, A:K.254, A:R.268 PO4.11: 5 residues within 4Å: Chain B: K.170, K.254, R.268, L.271 Ligands: PO4.3 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.254 Salt bridges: B:K.170, B:K.254, B:R.268 PO4.16: 3 residues within 4Å: Chain C: K.170, N.180 Chain D: R.148 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Water bridges: D:R.148 Salt bridges: D:R.148, C:K.170 Hydrogen bonds: C:N.180 PO4.17: 4 residues within 4Å: Chain C: R.148 Chain D: K.170, N.180 Ligands: PO4.25 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.180 Salt bridges: D:K.170, C:R.148 PO4.18: 5 residues within 4Å: Chain C: K.170, K.254, R.268, L.271 Ligands: NAD.15 3 PLIP interactions: 3 interactions with chain C Salt bridges: C:K.170, C:K.254, C:R.268 PO4.25: 5 residues within 4Å: Chain D: K.170, K.254, R.268, L.271 Ligands: PO4.17 4 PLIP interactions: 4 interactions with chain D Water bridges: D:K.254 Salt bridges: D:K.170, D:K.254, D:R.268

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

CL.5: 3 residues within 4Å: Chain A: Q.308, D.314, A.315 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: K.351 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: L.94 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: P.202, A.203 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: E.101, Q.102 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: P.335, E.336 Ligand excluded by PLIP CL.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain C: Q.308, D.314, A.315 Ligand excluded by PLIP CL.20: 1 residues within 4Å: Chain C: K.351 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain C: L.94 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain C: P.202, A.203 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain D: E.101, Q.102 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain D: P.335, E.336 Ligand excluded by PLIP CL.28: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.9: 5 residues within 4Å: Chain A: L.312, T.364 Chain C: L.312, T.364 Ligands: NA.23 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.364 NA.23: 5 residues within 4Å: Chain A: L.312, T.364 Chain C: L.312, T.364 Ligands: NA.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.364

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minasov, G. et al., 2.5 Angstrom Resolution Crystal Structure of 3-Dehydroquinate Synthase (aroB) from Vibrio cholerae. TO BE PUBLISHED

Release Date

2010-09-08

Peptides

3-dehydroquinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

3-dehydroquinate synthase

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