SMTL ID : 1j2y.1

Crystal structure of the type II 3-dehydroquinase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-12-mer

Ligands

12 x DQA: 1,3,4-TRIHYDROXY-5-OXO-CYCLOHEXANECARBOXYLIC ACID(Non-covalent)

DQA.1: 13 residues within 4Å: Chain A: R.17, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, I.106, R.109, R.113 Chain E: D.89 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.22, A:I.106 Hydrogen bonds: A:N.76, A:G.78, A:L.103, A:T.104, A:R.113, A:R.113 Water bridges: A:R.17, A:A.79 Salt bridges: A:H.102 DQA.2: 13 residues within 4Å: Chain B: R.17, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, I.106, R.109, R.113 Chain G: D.89 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.22, B:I.106 Hydrogen bonds: B:N.76, B:G.78, B:L.103, B:T.104, B:R.113, B:R.113 Water bridges: B:R.17, B:A.79 Salt bridges: B:H.102 DQA.3: 13 residues within 4Å: Chain C: R.17, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, I.106, R.109, R.113 Chain H: D.89 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:Y.22, C:I.106 Hydrogen bonds: C:Y.22, C:N.76, C:G.78, C:H.102, C:L.103, C:T.104, C:R.113, C:R.113 Water bridges: C:N.10, C:R.17 Salt bridges: C:H.102 DQA.4: 13 residues within 4Å: Chain D: R.17, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, I.106, R.109, R.113 Chain F: D.89 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:Y.22, D:I.106 Hydrogen bonds: D:Y.22, D:N.76, D:G.78, D:H.102, D:L.103, D:T.104, D:R.113, D:R.113 Water bridges: D:N.10, D:R.17 Salt bridges: D:H.102 DQA.5: 13 residues within 4Å: Chain E: R.17, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, I.106, R.109, R.113 Chain I: D.89 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:Y.22, E:I.106 Hydrogen bonds: E:Y.22, E:N.76, E:G.78, E:H.102, E:L.103, E:T.104, E:R.113, E:R.113 Water bridges: E:N.10, E:R.17 Salt bridges: E:H.102 DQA.6: 13 residues within 4Å: Chain F: R.17, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, I.106, R.109, R.113 Chain K: D.89 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:Y.22, F:I.106 Hydrogen bonds: F:N.76, F:G.78, F:L.103, F:T.104, F:R.113, F:R.113 Water bridges: F:R.17, F:A.79 Salt bridges: F:H.102 DQA.7: 13 residues within 4Å: Chain G: R.17, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, I.106, R.109, R.113 Chain L: D.89 13 PLIP interactions: 13 interactions with chain G Hydrophobic interactions: G:Y.22, G:I.106 Hydrogen bonds: G:Y.22, G:N.76, G:G.78, G:H.102, G:L.103, G:T.104, G:R.113, G:R.113 Water bridges: G:N.10, G:R.17 Salt bridges: G:H.102 DQA.8: 13 residues within 4Å: Chain H: R.17, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, I.106, R.109, R.113 Chain J: D.89 11 PLIP interactions: 11 interactions with chain H Hydrophobic interactions: H:Y.22, H:I.106 Hydrogen bonds: H:N.76, H:G.78, H:L.103, H:T.104, H:R.113, H:R.113 Water bridges: H:R.17, H:A.79 Salt bridges: H:H.102 DQA.9: 13 residues within 4Å: Chain A: D.89 Chain I: R.17, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, I.106, R.109, R.113 13 PLIP interactions: 13 interactions with chain I Hydrophobic interactions: I:Y.22, I:I.106 Hydrogen bonds: I:Y.22, I:N.76, I:G.78, I:H.102, I:L.103, I:T.104, I:R.113, I:R.113 Water bridges: I:R.17, I:A.79 Salt bridges: I:H.102 DQA.10: 13 residues within 4Å: Chain C: D.89 Chain J: R.17, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, I.106, R.109, R.113 11 PLIP interactions: 11 interactions with chain J Hydrophobic interactions: J:Y.22, J:I.106 Hydrogen bonds: J:N.76, J:G.78, J:L.103, J:T.104, J:R.113, J:R.113 Water bridges: J:N.10, J:R.17 Salt bridges: J:H.102 DQA.11: 13 residues within 4Å: Chain D: D.89 Chain K: R.17, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, I.106, R.109, R.113 11 PLIP interactions: 11 interactions with chain K Hydrophobic interactions: K:Y.22, K:I.106 Hydrogen bonds: K:N.76, K:G.78, K:L.103, K:T.104, K:R.113, K:R.113 Water bridges: K:N.10, K:R.17 Salt bridges: K:H.102 DQA.12: 13 residues within 4Å: Chain B: D.89 Chain L: R.17, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, I.106, R.109, R.113 13 PLIP interactions: 13 interactions with chain L Hydrophobic interactions: L:Y.22, L:I.106 Hydrogen bonds: L:Y.22, L:N.76, L:G.78, L:H.102, L:L.103, L:T.104, L:R.113, L:R.113 Water bridges: L:R.17, L:A.79 Salt bridges: L:H.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, B.I. et al., Crystal structure of the type II 3-dehydroquinase from Helicobacter pylori. Proteins (2003)

Release Date

2003-06-24

Peptides

3-dehydroquinate dehydratase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

3-dehydroquinate dehydratase

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