SMTL ID : 6lk2.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 24 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: 7LH.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:N.55, A:D.84, A:E.86, A:K.89, A:G.118, A:V.119, A:T.143, A:N.165, A:T.185, A:T.185, A:K.239, A:K.239 Water bridges: A:D.84, A:K.89, A:D.122, A:K.155, A:N.159 NAD.6: 26 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, S.146, D.149, S.150, K.155, N.165, C.182, T.185, L.186, P.187, E.190, K.239 Ligands: 7LH.8 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:N.55, B:D.84, B:E.86, B:K.89, B:G.117, B:G.118, B:V.119, B:T.143, B:T.143, B:S.146, B:N.165, B:T.185, B:K.239, B:K.239 Water bridges: B:E.86, B:N.159

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.149, E.197, H.261, H.278 Ligands: 7LH.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.197, A:H.261, A:H.278, H2O.2 MG.7: 5 residues within 4Å: Chain B: D.149, E.197, H.261, H.278 Ligands: 7LH.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.197, B:E.197, B:H.261, B:H.278, H2O.6

2 x 7LH: (1R,3R,4S,5R)-3-[3-[3,4-bis(oxidanyl)phenyl]propanoyloxy]-1,4,5-tris(oxidanyl)cyclohexane-1-carboxylic acid(Non-covalent)

7LH.3: 14 residues within 4Å: Chain A: D.149, K.155, E.197, K.200, K.239, R.254, L.257, N.258, H.261, T.262, H.265, H.278 Ligands: NAD.1, MG.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:H.261, A:H.265 Hydrogen bonds: A:K.200, A:K.200, A:T.262 Water bridges: A:N.165, A:K.239 Salt bridges: A:K.155, A:K.239, A:R.254 7LH.8: 13 residues within 4Å: Chain B: D.149, K.155, N.165, E.197, K.239, R.254, L.257, N.258, H.261, H.265, H.278 Ligands: NAD.6, MG.7 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.165, B:L.257, B:N.258 Salt bridges: B:K.155, B:K.239, B:R.254

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

EDO.4: 6 residues within 4Å: Chain A: T.18, V.19, T.20, A.240, Q.241, A.244 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.20

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

PEG.5: 3 residues within 4Å: Chain A: G.47, G.74, K.76 No protein-ligand interaction detected (PLIP)

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
B

B
D

3-dehydroquinate synthase

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