SMTL ID : 6hsu.1

The crystal structure of type II Dehydroquinase from Psychromonas ingrahamii 37, crystal form 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-12-mer

Ligands

12 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.1: 10 residues within 4Å: Chain A: N.80, A.82, A.83, T.85, H.86, H.106, L.107, S.108, R.113, R.117 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain G Hydrogen bonds: A:N.80, A:A.82, A:T.85, A:H.106, A:L.107, A:S.108, A:S.108, A:R.113 Water bridges: A:A.83, A:R.113, G:D.93, G:D.93 Salt bridges: A:H.86, A:H.106, A:R.117 TLA.2: 12 residues within 4Å: Chain B: N.80, A.82, A.83, T.85, H.86, H.106, L.107, S.108, V.110, R.113, R.117 Chain J: D.93 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain J Hydrogen bonds: B:N.80, B:N.80, B:A.82, B:T.85, B:H.106, B:L.107, B:S.108, J:D.93 Water bridges: B:A.83, B:R.113, B:R.113 Salt bridges: B:H.86, B:H.106, B:H.106, B:R.117 TLA.4: 11 residues within 4Å: Chain C: N.80, A.82, A.83, T.85, H.86, H.106, L.107, S.108, R.113, R.117 Chain D: D.93 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:N.80, C:A.82, C:H.106, C:L.107, C:S.108, C:S.108, D:D.93 Water bridges: C:A.83, C:R.113, C:R.113, C:R.113 Salt bridges: C:H.86, C:H.106, C:H.106, C:R.117 TLA.5: 11 residues within 4Å: Chain D: N.80, A.82, A.83, T.85, H.86, H.106, L.107, S.108, V.110, R.113, R.117 14 PLIP interactions: 12 interactions with chain D, 2 interactions with chain I Hydrogen bonds: D:N.80, D:N.80, D:A.82, D:T.85, D:L.107, D:S.108, I:D.93, I:D.93 Water bridges: D:A.83, D:R.113, D:R.113 Salt bridges: D:H.86, D:H.106, D:R.117 TLA.6: 12 residues within 4Å: Chain E: L.18, N.80, A.82, A.83, T.85, H.86, H.106, L.107, S.108, V.110, R.113, R.117 12 PLIP interactions: 10 interactions with chain E, 2 interactions with chain K Hydrogen bonds: E:N.80, E:A.82, E:L.107, E:S.108, E:S.108 Water bridges: E:A.83, E:R.113, K:D.93, K:D.93 Salt bridges: E:H.86, E:H.106, E:R.117 TLA.7: 11 residues within 4Å: Chain B: D.93 Chain F: N.80, A.82, A.83, H.86, H.106, L.107, S.108, V.110, R.113, R.117 14 PLIP interactions: 13 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:N.80, F:N.80, F:A.82, F:H.106, F:L.107, F:S.108, B:D.93 Water bridges: F:A.83, F:R.113, F:R.113 Salt bridges: F:H.86, F:H.106, F:H.106, F:R.117 TLA.8: 10 residues within 4Å: Chain G: N.80, A.82, A.83, H.86, H.106, L.107, S.108, V.110, R.113, R.117 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:N.80, G:N.80, G:A.82, G:L.107, G:S.108 Salt bridges: G:H.86, G:H.106, G:H.106, G:R.117 TLA.9: 10 residues within 4Å: Chain H: N.80, A.82, A.83, T.85, H.86, H.106, L.107, S.108, R.113, R.117 15 PLIP interactions: 13 interactions with chain H, 2 interactions with chain A Hydrogen bonds: H:N.80, H:N.80, H:A.82, H:T.85, H:T.85, H:H.106, H:L.107, H:S.108, A:D.93, A:D.93 Water bridges: H:A.83 Salt bridges: H:H.86, H:H.106, H:H.106, H:R.117 TLA.10: 11 residues within 4Å: Chain C: D.93 Chain I: N.80, A.82, A.83, H.86, H.106, L.107, S.108, V.110, R.113, R.117 16 PLIP interactions: 15 interactions with chain I, 1 interactions with chain C Hydrogen bonds: I:N.80, I:A.82, I:T.85, I:H.106, I:L.107, I:S.108, I:S.108, C:D.93 Water bridges: I:A.83, I:R.113, I:R.113 Salt bridges: I:H.86, I:H.106, I:H.106, I:R.113, I:R.117 TLA.11: 11 residues within 4Å: Chain F: D.93 Chain J: N.80, A.82, A.83, T.85, H.86, H.106, L.107, S.108, R.113, R.117 17 PLIP interactions: 15 interactions with chain J, 2 interactions with chain F Hydrogen bonds: J:N.80, J:N.80, J:A.82, J:T.85, J:T.85, J:L.107, J:S.108, F:D.93, F:D.93 Water bridges: J:A.83, J:R.113, J:R.113, J:R.117 Salt bridges: J:H.86, J:H.106, J:H.106, J:R.117 TLA.12: 11 residues within 4Å: Chain K: N.80, A.82, A.83, H.86, H.106, L.107, S.108, V.110, R.113, R.117 Chain L: D.93 11 PLIP interactions: 10 interactions with chain K, 1 interactions with chain L Hydrogen bonds: K:N.80, K:A.82, K:L.107, K:S.108, K:S.108, L:D.93 Water bridges: K:A.83 Salt bridges: K:H.86, K:H.106, K:H.106, K:R.117 TLA.14: 12 residues within 4Å: Chain L: L.18, N.80, A.82, A.83, T.85, H.86, H.106, L.107, S.108, V.110, R.113, R.117 10 PLIP interactions: 9 interactions with chain L, 1 interactions with chain E Hydrogen bonds: L:N.80, L:A.82, L:L.107, L:S.108, L:S.108, E:D.93 Water bridges: L:A.83 Salt bridges: L:H.86, L:H.106, L:R.117

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain B: D.43, E.44, L.47 4 PLIP interactions: 4 interactions with chain B Water bridges: B:D.43, B:D.43, B:E.44, B:E.44

1 x MPO: 3[N-MORPHOLINO]PROPANE SULFONIC ACID(Non-covalent)

MPO.13: 6 residues within 4Å: Chain K: Q.6, K.9, E.72, K.73, I.74, D.75 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:Q.6 Salt bridges: K:D.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lapthorn, A.J. et al., The crystal structure of type II Dehydroquinase from Psychromonas ingrahamii 37. To Be Published

Release Date

2019-10-23

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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