SMTL ID : 1v1j.1

Crystal structure of type II Dehydroquintae Dehydratase from Streptomyces coelicolor in complex with 3-fluoro

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-12-mer

Ligands

12 x FA3: 2-ANHYDRO-3-FLUORO-QUINIC ACID(Non-covalent)

FA3.1: 11 residues within 4Å: Chain A: Y.29, N.80, A.82, A.83, H.86, H.107, I.108, S.109, I.111, R.118 Chain B: D.93 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.29, A:A.82, A:I.111 Hydrogen bonds: A:N.80, A:A.82, A:H.86, A:H.107, A:I.108, A:S.109, A:S.109, A:R.118 Water bridges: A:A.83 Salt bridges: A:H.107 FA3.3: 11 residues within 4Å: Chain B: Y.29, N.80, A.82, A.83, H.86, H.107, I.108, S.109, I.111, R.118 Chain C: D.93 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Y.29, B:A.82, B:I.111 Hydrogen bonds: B:N.80, B:A.82, B:H.86, B:I.108, B:S.109, B:S.109, B:R.118 Salt bridges: B:H.107 Water bridges: C:D.93 FA3.4: 11 residues within 4Å: Chain A: D.93 Chain C: Y.29, N.80, A.82, A.83, H.86, H.107, I.108, S.109, I.111, R.118 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:Y.29, C:A.82, C:I.111 Hydrogen bonds: C:N.80, C:A.82, C:H.86, C:H.107, C:I.108, C:S.109, C:S.109, C:R.118 Salt bridges: C:H.107 Water bridges: A:D.93 FA3.5: 12 residues within 4Å: Chain D: Y.29, N.80, A.82, A.83, H.86, H.107, I.108, S.109, I.111, R.114, R.118 Chain E: D.93 12 PLIP interactions: 1 interactions with chain E, 11 interactions with chain D Water bridges: E:D.93 Hydrophobic interactions: D:Y.29, D:A.82, D:I.111 Hydrogen bonds: D:N.80, D:A.82, D:H.86, D:I.108, D:S.109, D:S.109, D:R.118 Salt bridges: D:H.107 FA3.6: 11 residues within 4Å: Chain E: Y.29, N.80, A.82, A.83, H.86, H.107, I.108, S.109, I.111, R.118 Chain F: D.93 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:Y.29, E:A.82, E:I.111 Hydrogen bonds: E:N.80, E:A.82, E:H.86, E:H.107, E:I.108, E:S.109, E:S.109, E:R.118 Water bridges: E:A.83 Salt bridges: E:H.107 FA3.8: 11 residues within 4Å: Chain D: D.93 Chain F: Y.29, N.80, A.82, A.83, H.86, H.107, I.108, S.109, I.111, R.118 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:Y.29, F:A.82, F:I.111 Hydrogen bonds: F:N.80, F:A.82, F:H.86, F:H.107, F:I.108, F:S.109, F:S.109, F:R.118 Water bridges: F:A.83 Salt bridges: F:H.107 FA3.9: 11 residues within 4Å: Chain G: Y.29, N.80, A.82, A.83, H.86, H.107, I.108, S.109, I.111, R.118 Chain H: D.93 12 PLIP interactions: 1 interactions with chain H, 11 interactions with chain G Water bridges: H:D.93 Hydrophobic interactions: G:Y.29, G:A.82, G:I.111 Hydrogen bonds: G:N.80, G:A.82, G:H.86, G:I.108, G:S.109, G:S.109, G:R.118 Salt bridges: G:H.107 FA3.10: 11 residues within 4Å: Chain H: Y.29, N.80, A.82, A.83, H.86, H.107, I.108, S.109, I.111, R.118 Chain I: D.93 12 PLIP interactions: 1 interactions with chain I, 11 interactions with chain H Water bridges: I:D.93 Hydrophobic interactions: H:Y.29, H:A.82, H:I.111 Hydrogen bonds: H:N.80, H:A.82, H:H.86, H:I.108, H:S.109, H:S.109, H:R.118 Salt bridges: H:H.107 FA3.11: 11 residues within 4Å: Chain G: D.93 Chain I: Y.29, N.80, A.82, A.83, H.86, H.107, I.108, S.109, I.111, R.118 13 PLIP interactions: 13 interactions with chain I Hydrophobic interactions: I:Y.29, I:A.82, I:I.111 Hydrogen bonds: I:N.80, I:A.82, I:H.86, I:H.107, I:I.108, I:S.109, I:S.109, I:R.118 Water bridges: I:A.83 Salt bridges: I:H.107 FA3.13: 11 residues within 4Å: Chain J: Y.29, N.80, A.82, A.83, H.86, H.107, I.108, S.109, I.111, R.118 Chain K: D.93 12 PLIP interactions: 12 interactions with chain J Hydrophobic interactions: J:Y.29, J:A.82, J:I.111 Hydrogen bonds: J:N.80, J:A.82, J:H.86, J:I.108, J:S.109, J:S.109, J:R.118 Water bridges: J:A.83 Salt bridges: J:H.107 FA3.14: 11 residues within 4Å: Chain K: Y.29, N.80, A.82, A.83, H.86, H.107, I.108, S.109, I.111, R.118 Chain L: D.93 12 PLIP interactions: 1 interactions with chain L, 11 interactions with chain K Water bridges: L:D.93 Hydrophobic interactions: K:Y.29, K:A.82, K:I.111 Hydrogen bonds: K:N.80, K:A.82, K:H.86, K:I.108, K:S.109, K:S.109, K:R.118 Salt bridges: K:H.107 FA3.16: 11 residues within 4Å: Chain J: D.93 Chain L: Y.29, N.80, A.82, A.83, H.86, H.107, I.108, S.109, I.111, R.118 13 PLIP interactions: 13 interactions with chain L Hydrophobic interactions: L:Y.29, L:A.82, L:I.111 Hydrogen bonds: L:N.80, L:A.82, L:H.86, L:H.107, L:I.108, L:S.109, L:S.109, L:R.118 Water bridges: L:A.83 Salt bridges: L:H.107

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 10 residues within 4Å: Chain A: E.60, T.87, S.88 Chain B: E.60, T.87, S.88 Chain C: E.60, Y.84, T.87, S.88 8 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: C:E.60, C:T.87, A:T.87, A:T.87, B:T.87 Water bridges: C:V.89, A:E.60, B:V.89 TRS.7: 10 residues within 4Å: Chain D: E.60, T.87, S.88 Chain E: E.60, Y.84, T.87, S.88 Chain F: E.60, T.87, S.88 7 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E, 2 interactions with chain D Hydrogen bonds: F:T.87, F:T.87, E:T.87, D:E.60, D:T.87 Water bridges: F:V.89, E:E.60 TRS.12: 10 residues within 4Å: Chain G: E.60, T.87, S.88 Chain H: E.60, T.87, S.88 Chain I: E.60, Y.84, T.87, S.88 9 PLIP interactions: 3 interactions with chain I, 3 interactions with chain G, 3 interactions with chain H Hydrogen bonds: I:T.87, I:T.87, G:T.87, G:T.87, H:E.60, H:T.87 Water bridges: I:E.60, G:V.89, H:V.89 TRS.15: 10 residues within 4Å: Chain J: E.60, T.87, S.88 Chain K: E.60, Y.84, T.87, S.88 Chain L: E.60, T.87, S.88 8 PLIP interactions: 4 interactions with chain L, 3 interactions with chain J, 1 interactions with chain K Hydrogen bonds: L:T.87, L:T.87, J:E.60, J:T.87, J:T.87, K:T.87 Water bridges: L:E.60, L:V.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Frederickson, M. et al., (1R,4S,5R)-3-Fluoro-1,4,5-Trihydroxy-2-Cyclohexene-1-Carboxylic Acid: The Fluoro Analogue of the Enolate Intermediate in the Reaction Catalyzed by Type II Dehydroquinases. Org.Biomol.Chem. (2004)

Release Date

2005-01-26

Peptides

3-DEHYDROQUINATE DEHYDRATASE: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

3-DEHYDROQUINATE DEHYDRATASE

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