SMTL ID : 1gtz.1

Structure of STREPTOMYCES COELICOLOR TYPE II DEHYDROQUINASE R23A MUTANT IN COMPLEX WITH DEHYDROSHIKIMATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-12-mer

Ligands

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

TRS.1: 10 residues within 4Å: Chain A: E.59, Y.83, T.86, S.87 Chain B: E.59, T.86, S.87 Chain C: E.59, T.86, S.87 9 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:E.59, A:T.86, A:T.86, B:T.86, B:T.86, C:T.86 Water bridges: A:E.59, B:V.88, C:V.88 TRS.5: 9 residues within 4Å: Chain D: E.59, T.86, S.87 Chain E: E.59, T.86, S.87 Chain F: E.59, T.86, S.87 9 PLIP interactions: 4 interactions with chain F, 2 interactions with chain D, 3 interactions with chain E Hydrogen bonds: F:T.86, F:T.86, D:T.86, E:E.59, E:T.86 Water bridges: F:E.59, F:V.88, D:V.88, E:V.88 TRS.9: 9 residues within 4Å: Chain G: E.59, T.86, S.87 Chain H: E.59, T.86, S.87 Chain I: E.59, T.86, S.87 9 PLIP interactions: 2 interactions with chain H, 5 interactions with chain I, 2 interactions with chain G Hydrogen bonds: H:T.86, I:E.59, I:T.86, I:T.86, G:T.86 Water bridges: H:V.88, I:E.59, I:V.88, G:V.88 TRS.13: 9 residues within 4Å: Chain J: E.59, T.86, S.87 Chain K: E.59, T.86, S.87 Chain L: E.59, T.86, S.87 9 PLIP interactions: 2 interactions with chain J, 5 interactions with chain L, 2 interactions with chain K Hydrogen bonds: J:T.86, L:E.59, L:T.86, L:T.86, K:T.86 Water bridges: J:V.88, L:E.59, L:V.88, K:V.88

12 x DHK: 3-DEHYDROSHIKIMATE(Non-covalent)

DHK.2: 11 residues within 4Å: Chain A: Y.28, N.79, A.81, A.82, H.85, H.106, I.107, S.108, I.110, R.117 Chain B: D.92 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.28, A:I.110 Hydrogen bonds: A:N.79, A:N.79, A:A.82, A:H.85, A:I.107, A:S.108, A:R.117, B:D.92 Water bridges: B:D.92, B:D.92 DHK.3: 11 residues within 4Å: Chain B: Y.28, N.79, A.81, A.82, H.85, H.106, I.107, S.108, I.110, R.117 Chain C: D.92 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Y.28, B:A.81, B:I.110 Hydrogen bonds: B:N.79, B:N.79, B:A.82, B:H.85, B:I.107, B:S.108, B:R.117, C:D.92 DHK.4: 12 residues within 4Å: Chain A: D.92 Chain C: Y.28, N.79, A.81, A.82, H.85, H.106, I.107, S.108, I.110, R.113, R.117 12 PLIP interactions: 2 interactions with chain A, 10 interactions with chain C Hydrogen bonds: A:D.92, A:D.92, C:N.79, C:N.79, C:H.85, C:I.107, C:S.108, C:R.117 Hydrophobic interactions: C:Y.28, C:I.110 Water bridges: C:A.82, C:A.82 DHK.6: 11 residues within 4Å: Chain D: Y.28, N.79, A.81, A.82, H.85, H.106, I.107, S.108, I.110, R.117 Chain E: D.92 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:Y.28, D:I.110 Hydrogen bonds: D:N.79, D:N.79, D:A.82, D:H.85, D:I.107, D:S.108, D:R.117, E:D.92 DHK.7: 11 residues within 4Å: Chain E: Y.28, N.79, A.81, A.82, H.85, H.106, I.107, S.108, I.110, R.117 Chain F: D.92 12 PLIP interactions: 10 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:Y.28, E:I.110 Hydrogen bonds: E:N.79, E:N.79, E:A.82, E:H.85, E:I.107, E:S.108, E:R.117, F:D.92, F:D.92 Salt bridges: E:H.106 DHK.8: 12 residues within 4Å: Chain D: D.92 Chain F: Y.28, N.79, A.81, A.82, H.85, H.106, I.107, S.108, I.110, R.113, R.117 10 PLIP interactions: 9 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: F:Y.28, F:I.110 Hydrogen bonds: F:N.79, F:N.79, F:A.82, F:H.85, F:I.107, F:S.108, F:R.117, D:D.92 DHK.10: 11 residues within 4Å: Chain G: Y.28, N.79, A.81, A.82, H.85, H.106, I.107, S.108, I.110, R.117 Chain H: D.92 10 PLIP interactions: 8 interactions with chain G, 2 interactions with chain H Hydrophobic interactions: G:Y.28, G:I.110 Hydrogen bonds: G:N.79, G:N.79, G:A.82, G:I.107, G:S.108, G:R.117, H:D.92, H:D.92 DHK.11: 12 residues within 4Å: Chain H: Y.28, N.79, A.81, A.82, H.85, H.106, I.107, S.108, I.110, R.113, R.117 Chain I: D.92 12 PLIP interactions: 10 interactions with chain H, 2 interactions with chain I Hydrophobic interactions: H:Y.28, H:I.110 Hydrogen bonds: H:N.79, H:N.79, H:A.82, H:H.85, H:I.107, H:S.108, H:R.117, I:D.92, I:D.92 Salt bridges: H:H.106 DHK.12: 12 residues within 4Å: Chain G: D.92 Chain I: Y.28, N.79, A.81, A.82, H.85, H.106, I.107, S.108, I.110, R.113, R.117 11 PLIP interactions: 10 interactions with chain I, 1 interactions with chain G Hydrophobic interactions: I:Y.28, I:A.81, I:I.110 Hydrogen bonds: I:N.79, I:N.79, I:A.82, I:H.85, I:I.107, I:S.108, I:R.117, G:D.92 DHK.14: 12 residues within 4Å: Chain J: Y.28, N.79, A.81, A.82, H.85, H.106, I.107, S.108, I.110, R.113, R.117 Chain K: D.92 10 PLIP interactions: 1 interactions with chain K, 9 interactions with chain J Hydrogen bonds: K:D.92, J:N.79, J:N.79, J:A.82, J:H.85, J:I.107, J:S.108, J:R.117 Hydrophobic interactions: J:Y.28, J:I.110 DHK.15: 11 residues within 4Å: Chain K: Y.28, N.79, A.81, A.82, H.85, H.106, I.107, S.108, I.110, R.117 Chain L: D.92 10 PLIP interactions: 8 interactions with chain K, 2 interactions with chain L Hydrophobic interactions: K:Y.28, K:I.110 Hydrogen bonds: K:N.79, K:N.79, K:A.82, K:I.107, K:S.108, K:R.117, L:D.92, L:D.92 DHK.16: 11 residues within 4Å: Chain J: D.92 Chain L: Y.28, N.79, A.81, A.82, H.85, H.106, I.107, S.108, I.110, R.117 9 PLIP interactions: 8 interactions with chain L, 1 interactions with chain J Hydrophobic interactions: L:Y.28, L:I.110 Hydrogen bonds: L:N.79, L:N.79, L:A.82, L:I.107, L:S.108, L:R.117, J:D.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roszak, A.W. et al., The Structure and Mechanism of the Type II Dehydroquinase from Streptomyces Coelicolor. Structure (2002)

Release Date

2002-06-27

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