SMTL ID : 6hsq.1

The crystal structure of type II Dehydroquinase from Psychromonas ingrahamii 37 crystal form 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

homo-12-mer

Ligands

24 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 6 residues within 4Å: Chain A: L.18, N.80, H.106, L.107, S.108 Ligands: GOL.3 Ligand excluded by PLIP SO4.2: 1 residues within 4Å: Chain A: R.59 Ligand excluded by PLIP SO4.4: 6 residues within 4Å: Chain B: L.18, N.80, H.106, L.107, S.108 Ligands: GOL.6 Ligand excluded by PLIP SO4.5: 1 residues within 4Å: Chain B: R.59 Ligand excluded by PLIP SO4.7: 6 residues within 4Å: Chain C: L.18, N.80, H.106, L.107, S.108 Ligands: GOL.9 Ligand excluded by PLIP SO4.8: 1 residues within 4Å: Chain C: R.59 Ligand excluded by PLIP SO4.10: 6 residues within 4Å: Chain D: L.18, N.80, H.106, L.107, S.108 Ligands: GOL.12 Ligand excluded by PLIP SO4.11: 1 residues within 4Å: Chain D: R.59 Ligand excluded by PLIP SO4.13: 6 residues within 4Å: Chain E: L.18, N.80, H.106, L.107, S.108 Ligands: GOL.15 Ligand excluded by PLIP SO4.14: 1 residues within 4Å: Chain E: R.59 Ligand excluded by PLIP SO4.16: 6 residues within 4Å: Chain F: L.18, N.80, H.106, L.107, S.108 Ligands: GOL.18 Ligand excluded by PLIP SO4.17: 1 residues within 4Å: Chain F: R.59 Ligand excluded by PLIP SO4.19: 6 residues within 4Å: Chain G: L.18, N.80, H.106, L.107, S.108 Ligands: GOL.21 Ligand excluded by PLIP SO4.20: 1 residues within 4Å: Chain G: R.59 Ligand excluded by PLIP SO4.22: 6 residues within 4Å: Chain H: L.18, N.80, H.106, L.107, S.108 Ligands: GOL.24 Ligand excluded by PLIP SO4.23: 1 residues within 4Å: Chain H: R.59 Ligand excluded by PLIP SO4.25: 6 residues within 4Å: Chain I: L.18, N.80, H.106, L.107, S.108 Ligands: GOL.27 Ligand excluded by PLIP SO4.26: 1 residues within 4Å: Chain I: R.59 Ligand excluded by PLIP SO4.28: 6 residues within 4Å: Chain J: L.18, N.80, H.106, L.107, S.108 Ligands: GOL.30 Ligand excluded by PLIP SO4.29: 1 residues within 4Å: Chain J: R.59 Ligand excluded by PLIP SO4.31: 6 residues within 4Å: Chain K: L.18, N.80, H.106, L.107, S.108 Ligands: GOL.33 Ligand excluded by PLIP SO4.32: 1 residues within 4Å: Chain K: R.59 Ligand excluded by PLIP SO4.34: 6 residues within 4Å: Chain L: L.18, N.80, H.106, L.107, S.108 Ligands: GOL.36 Ligand excluded by PLIP SO4.35: 1 residues within 4Å: Chain L: R.59 Ligand excluded by PLIP

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: N.80, A.82, A.83, H.86, H.106, V.110, R.113, R.117 Chain B: D.93 Ligands: SO4.1 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.106, A:R.113, A:R.113, A:R.117, B:D.93 GOL.6: 10 residues within 4Å: Chain B: N.80, A.82, A.83, H.86, H.106, V.110, R.113, R.117 Chain C: D.93 Ligands: SO4.4 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:H.106, B:R.113, B:R.117, C:D.93 Water bridges: B:R.113 GOL.9: 10 residues within 4Å: Chain A: D.93 Chain C: N.80, A.82, A.83, H.86, H.106, V.110, R.113, R.117 Ligands: SO4.7 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.80, C:H.106, C:R.113, C:R.113, C:R.117 Water bridges: A:D.93 GOL.12: 10 residues within 4Å: Chain D: N.80, A.82, A.83, H.86, H.106, V.110, R.113, R.117 Chain L: D.93 Ligands: SO4.10 8 PLIP interactions: 1 interactions with chain L, 7 interactions with chain D Hydrogen bonds: L:D.93, D:N.80, D:H.106, D:R.113, D:R.117, D:R.117 Water bridges: D:R.113, D:R.113 GOL.15: 10 residues within 4Å: Chain E: N.80, A.82, A.83, H.86, H.106, V.110, R.113, R.117 Chain F: D.93 Ligands: SO4.13 5 PLIP interactions: 1 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:D.93, E:H.106, E:R.113, E:R.113, E:R.117 GOL.18: 10 residues within 4Å: Chain F: N.80, A.82, A.83, H.86, H.106, V.110, R.113, R.117 Chain G: D.93 Ligands: SO4.16 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:N.80, F:H.106, F:R.113, F:R.117, G:D.93 Water bridges: F:R.113 GOL.21: 10 residues within 4Å: Chain E: D.93 Chain G: N.80, A.82, A.83, H.86, H.106, V.110, R.113, R.117 Ligands: SO4.19 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain E Hydrogen bonds: G:H.106, G:R.113, G:R.113, G:R.117 Water bridges: E:D.93 GOL.24: 10 residues within 4Å: Chain D: D.93 Chain H: N.80, A.82, A.83, H.86, H.106, V.110, R.113, R.117 Ligands: SO4.22 7 PLIP interactions: 6 interactions with chain H, 1 interactions with chain D Hydrogen bonds: H:H.106, H:R.113, H:R.117, H:R.117, D:D.93 Water bridges: H:R.113, H:R.113 GOL.27: 10 residues within 4Å: Chain I: N.80, A.82, A.83, H.86, H.106, V.110, R.113, R.117 Chain J: D.93 Ligands: SO4.25 6 PLIP interactions: 5 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:N.80, I:H.106, I:R.113, I:R.113, I:R.117, J:D.93 GOL.30: 10 residues within 4Å: Chain J: N.80, A.82, A.83, H.86, H.106, V.110, R.113, R.117 Chain K: D.93 Ligands: SO4.28 6 PLIP interactions: 1 interactions with chain K, 5 interactions with chain J Hydrogen bonds: K:D.93, J:N.80, J:H.106, J:R.113, J:R.117 Water bridges: J:R.113 GOL.33: 10 residues within 4Å: Chain I: D.93 Chain K: N.80, A.82, A.83, H.86, H.106, V.110, R.113, R.117 Ligands: SO4.31 6 PLIP interactions: 1 interactions with chain I, 5 interactions with chain K Water bridges: I:D.93 Hydrogen bonds: K:N.80, K:H.106, K:R.113, K:R.113, K:R.117 GOL.36: 10 residues within 4Å: Chain H: D.93 Chain L: N.80, A.82, A.83, H.86, H.106, V.110, R.113, R.117 Ligands: SO4.34 7 PLIP interactions: 6 interactions with chain L, 1 interactions with chain H Hydrogen bonds: L:H.106, L:R.113, L:R.117, L:R.117, H:D.93 Water bridges: L:R.113, L:R.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lapthorn, A.J. et al., The crystal structure of type II Dehydroquinase from Butyrivibrio crossotus DSM 2876. 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
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

3-dehydroquinate dehydratase

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