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

Structure of 3-Dehydroquinate Synthase from Actinidia chinensis in complex with NAD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 8 residues within 4Å: Chain A: K.166, N.167, H.262, H.266, H.279 Ligands: PO4.2, NAD.4, GLY.6 7 PLIP interactions: 5 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:N.167, A:N.259, G.6, G.6 Salt bridges: A:H.262, A:H.266, A:H.279 PO4.2: 8 residues within 4Å: Chain A: K.157, N.167, N.259, H.266, K.338 Chain B: R.135 Ligands: PO4.1, GLY.6 9 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B, 3 Ligand-Ligand interactions Hydrogen bonds: A:N.167, A:N.259, G.6, G.6, G.6 Salt bridges: A:K.157, A:H.266, A:K.338, B:R.135 PO4.3: 10 residues within 4Å: Chain A: N.259, L.260, G.261, H.262, T.263, F.264, A.290, K.339, L.347, I.348 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.259, A:G.261, A:T.263, A:T.263, A:F.264, A:I.348, A:I.348, A:I.348 Salt bridges: A:K.339 PO4.7: 7 residues within 4Å: Chain B: N.167, E.199, H.262, H.266, H.279 Ligands: PO4.8, NAD.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.167 Salt bridges: B:H.262, B:H.266, B:H.279 PO4.8: 7 residues within 4Å: Chain A: R.135 Chain B: K.157, N.167, N.259, H.266, K.338 Ligands: PO4.7 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.167, B:N.259 Water bridges: B:H.266, B:K.338 Salt bridges: B:K.157, B:H.266, B:K.338, A:R.135 PO4.9: 10 residues within 4Å: Chain B: N.259, L.260, G.261, H.262, T.263, F.264, A.290, K.339, L.347, I.348 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.261, B:G.261, B:T.263, B:F.264, B:I.348, B:I.348 Salt bridges: B:K.339 PO4.10: 4 residues within 4Å: Chain B: Y.232, K.235, R.236, E.239 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.232 Salt bridges: B:K.235, B:R.236

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

NAD.4: 27 residues within 4Å: Chain A: N.55, T.57, V.58, Y.62, D.86, E.88, K.91, G.119, G.120, V.121, D.124, T.144, T.145, M.147, D.151, S.152, K.157, K.166, N.167, T.184, T.187, L.188, E.192, K.241, H.279 Ligands: PO4.1, GLY.6 25 PLIP interactions: 23 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:N.55, A:T.57, A:Y.62, A:Y.62, A:D.86, A:E.88, A:K.91, A:G.120, A:V.121, A:D.124, A:T.144, A:T.145, A:K.166, A:K.166, A:N.167, A:T.187, A:K.241, G.6, G.6 Water bridges: A:D.86, A:G.119, A:G.119, A:D.124, A:K.157, A:H.279 NAD.11: 26 residues within 4Å: Chain B: N.55, T.57, V.58, Y.62, D.86, E.88, K.91, G.119, G.120, V.121, D.124, T.144, T.145, M.147, D.151, S.152, K.157, K.166, N.167, T.184, T.187, L.188, E.192, K.241, H.279 Ligands: PO4.7 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:N.55, B:D.86, B:E.88, B:G.120, B:V.121, B:D.124, B:T.144, B:T.145, B:K.166, B:N.167, B:K.241, B:H.279 Water bridges: B:G.119, B:G.119, B:D.124, B:K.157

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 6 residues within 4Å: Chain A: K.331, A.335, G.343 Chain B: R.49, S.106, R.107 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.331

3 x GLY: GLYCINE(Non-covalent)

GLY.6: 8 residues within 4Å: Chain A: D.151, K.157, K.241, R.255, N.259 Ligands: PO4.1, PO4.2, NAD.4 9 PLIP interactions: 7 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:K.241, G.6, G.6 Water bridges: A:D.151, A:R.255, A:L.258 Salt bridges: A:K.157, A:K.241, A:R.255 GLY.15: 4 residues within 4Å: Chain B: N.186, T.187, L.188, R.225 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Ligand interactions Hydrogen bonds: B:D.190, G.15, G.15 Water bridges: B:D.190, G.15 Salt bridges: B:R.225 GLY.16: 4 residues within 4Å: Chain B: W.299, K.351, T.360, D.362 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Ligand interactions Salt bridges: B:K.351 Hydrogen bonds: G.16, G.16

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

PEG.12: 3 residues within 4Å: Chain B: T.270, G.271, M.329 No protein-ligand interaction detected (PLIP) PEG.13: 5 residues within 4Å: Chain A: L.164, S.332 Chain B: I.104, E.105, R.107 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.105, B:R.107 PEG.14: 5 residues within 4Å: Chain A: R.107 Chain B: K.331, A.335, V.340, G.343 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.331, A:R.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mittelstadt, G. et al., Biochemical and structural characterisation of dehydroquinate synthase from the New Zealand kiwifruit Actinidia chinensis. Arch. Biochem. Biophys. (2013)

Release Date

2013-08-21

Peptides

3-DEHYDROQUINATE SYNTHASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

3-DEHYDROQUINATE SYNTHASE

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