SMTL ID : 6lla.1 (1 other biounit)

Crystal structure of Providencia alcalifaciens 3-dehydroquinate synthase (DHQS) in complex with Mg2+ and NAD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 25 residues within 4Å: Chain A: N.55, T.57, L.58, D.84, E.86, K.89, G.117, G.118, V.119, D.122, T.142, T.143, L.145, D.149, S.150, K.155, N.165, C.182, T.185, L.186, P.187, E.190, K.239 Ligands: EDO.8, PEG.15 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:L.145, A:D.149 Hydrogen bonds: A:N.55, A:D.84, A:E.86, A:K.89, A:G.118, A:V.119, A:D.122, A:T.142, A:T.143, A:N.165, A:K.239, A:K.239 Water bridges: A:D.84, A:E.86, A:G.117, A:I.120, A:D.122, A:K.155, A:N.159 NAD.20: 25 residues within 4Å: Chain B: N.55, T.57, L.58, Y.62, D.84, E.86, K.89, G.117, G.118, V.119, D.122, T.142, T.143, L.145, D.149, S.150, K.155, N.165, C.182, T.185, L.186, P.187, E.190, K.239 Ligands: PEG.26 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:N.55, B:T.57, B:D.84, B:E.86, B:K.89, B:G.118, B:V.119, B:T.142, B:T.142, B:T.143, B:N.165, B:T.185, B:K.239, B:K.239 Water bridges: B:D.84, B:E.86, B:E.86, B:I.120, B:K.155

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.149, E.197, H.261, H.278 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.197, A:H.261, A:H.278, H2O.2, H2O.4, H2O.7 MG.21: 4 residues within 4Å: Chain B: D.149, E.197, H.261, H.278 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.197, B:H.261, B:H.278, H2O.14, H2O.17, H2O.18

15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: S.90, L.91, F.92, N.159, H.160, P.161 Chain B: N.95 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.91, B:N.95, B:N.95 EDO.4: 7 residues within 4Å: Chain A: D.22, R.24, F.170, Y.171, Q.172 Ligands: EDO.9, PEG.17 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.22, A:R.24, A:Q.172, A:Q.172 EDO.5: 5 residues within 4Å: Chain A: W.276, P.317, T.319, G.320, P.375 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.319, A:G.320 Water bridges: A:T.319, A:A.322 EDO.6: 5 residues within 4Å: Chain A: Q.38, D.39, F.41, L.44, S.73 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.39, A:D.39, A:F.41, A:S.73 EDO.7: 3 residues within 4Å: Chain A: S.211, W.212, E.215 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.211 Water bridges: A:S.211 EDO.8: 8 residues within 4Å: Chain A: G.121, D.122, F.137, Q.139, S.150, K.155, T.156 Ligands: NAD.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.139, A:S.150 Water bridges: A:D.122, A:Y.171 EDO.9: 4 residues within 4Å: Chain A: R.24, Y.171, Q.172 Ligands: EDO.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.24, A:Q.172, A:Q.172 EDO.10: 4 residues within 4Å: Chain A: K.291, E.294, L.295, A.372 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.294 Water bridges: A:K.291, A:A.372 EDO.11: 1 residues within 4Å: Chain A: E.270 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.323, A:K.323 EDO.12: 1 residues within 4Å: Chain A: H.64 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.64 EDO.13: 2 residues within 4Å: Chain A: Q.36, Q.37 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.36 EDO.22: 5 residues within 4Å: Chain B: L.253, L.256, H.354, S.355, E.356 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.355 EDO.23: 3 residues within 4Å: Chain B: R.24, Y.171, Q.172 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.24, B:Q.172 Water bridges: B:Q.172, B:Q.172, B:Q.172, B:P.173 EDO.24: 5 residues within 4Å: Chain B: T.18, V.19, T.20, A.240, A.244 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.18, B:T.20 EDO.25: 5 residues within 4Å: Chain A: R.133 Chain B: K.155, N.165 Ligands: PEG.16, PEG.26 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.155, B:K.155, B:N.165, A:R.133, A:R.133

7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.14: 5 residues within 4Å: Chain A: M.14, K.16, P.27, N.29, W.42 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.16, A:N.29 PEG.15: 7 residues within 4Å: Chain A: K.155, K.239, R.254, A.255, L.257, N.258 Ligands: NAD.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.239, A:K.239, A:R.254, A:N.258 Water bridges: A:K.155 PEG.16: 7 residues within 4Å: Chain A: R.108, Q.132, R.133 Chain B: K.164, N.165, M.166 Ligands: EDO.25 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.132 Water bridges: A:R.108 PEG.17: 3 residues within 4Å: Chain A: D.22, F.170 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.22 PEG.18: 1 residues within 4Å: Chain A: M.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.14 Water bridges: A:M.14 PEG.19: 5 residues within 4Å: Chain A: I.204, L.256, T.350, H.354, S.355 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.204, A:T.350, A:S.355 PEG.26: 7 residues within 4Å: Chain B: K.155, K.239, R.254, L.257, N.258 Ligands: NAD.20, EDO.25 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.152, B:K.239, B:R.254

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neetu, N. et al., Structural and Biochemical Analyses Reveal that Chlorogenic Acid Inhibits the Shikimate Pathway. J.Bacteriol. (2020)

Release Date

2020-07-29

Peptides

3-dehydroquinate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

3-dehydroquinate synthase

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