SMTL ID : 4civ.1

Crystal structure of Mycobacterium tuberculosis type 2 dehydroquinase in complex with (1R,4R,5R)-1,4,5-trihydroxy-3-hydroxymethylcyclohex-2-ene-1-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-12-mer

Ligands

12 x 48P: (1R,4R,5R)-1,4,5-trihydroxy-3-hydroxymethylcyclohex-2-ene-1-carboxylic acid(Non-covalent)

48P.1: 12 residues within 4Å: Chain A: R.19, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 Chain J: D.88 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.105 Hydrogen bonds: A:R.19, A:N.75, A:H.81, A:H.101, A:I.102, A:S.103, A:R.108, A:R.112 Water bridges: A:G.78 Salt bridges: A:R.19 48P.2: 12 residues within 4Å: Chain B: R.19, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 Chain G: D.88 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain G Hydrophobic interactions: B:V.105 Hydrogen bonds: B:R.19, B:N.75, B:H.81, B:H.101, B:I.102, B:S.103, B:R.108, B:R.112, G:D.88 Water bridges: B:G.78 Salt bridges: B:R.19 48P.3: 12 residues within 4Å: Chain B: D.88 Chain C: R.19, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:V.105 Hydrogen bonds: C:R.19, C:N.75, C:H.81, C:H.101, C:I.102, C:S.103, C:R.108, C:R.112 Water bridges: C:G.78 Salt bridges: C:R.19 48P.4: 12 residues within 4Å: Chain D: R.19, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 Chain F: D.88 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:V.105 Hydrogen bonds: D:R.19, D:N.75, D:H.81, D:H.101, D:I.102, D:S.103, D:R.108, D:R.112, F:D.88 Water bridges: D:G.78 Salt bridges: D:R.19 48P.5: 12 residues within 4Å: Chain E: R.19, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 Chain L: D.88 12 PLIP interactions: 11 interactions with chain E, 1 interactions with chain L Hydrophobic interactions: E:V.105 Hydrogen bonds: E:R.19, E:N.75, E:H.81, E:H.101, E:I.102, E:S.103, E:R.108, E:R.112, L:D.88 Water bridges: E:G.78 Salt bridges: E:R.19 48P.6: 12 residues within 4Å: Chain F: R.19, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 Chain H: D.88 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:V.105 Hydrogen bonds: F:R.19, F:N.75, F:H.81, F:H.101, F:I.102, F:S.103, F:R.108, F:R.112 Water bridges: F:G.78 Salt bridges: F:R.19 48P.7: 12 residues within 4Å: Chain C: D.88 Chain G: R.19, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 11 PLIP interactions: 11 interactions with chain G Hydrophobic interactions: G:V.105 Hydrogen bonds: G:R.19, G:N.75, G:H.81, G:H.101, G:I.102, G:S.103, G:R.108, G:R.112 Water bridges: G:G.78 Salt bridges: G:R.19 48P.8: 12 residues within 4Å: Chain D: D.88 Chain H: R.19, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 12 PLIP interactions: 11 interactions with chain H, 1 interactions with chain D Hydrophobic interactions: H:V.105 Hydrogen bonds: H:R.19, H:N.75, H:H.81, H:H.101, H:I.102, H:S.103, H:R.108, H:R.112, D:D.88 Water bridges: H:G.78 Salt bridges: H:R.19 48P.9: 12 residues within 4Å: Chain E: D.88 Chain I: R.19, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 12 PLIP interactions: 11 interactions with chain I, 1 interactions with chain E Hydrophobic interactions: I:V.105 Hydrogen bonds: I:R.19, I:N.75, I:H.81, I:H.101, I:I.102, I:S.103, I:R.108, I:R.112, E:D.88 Water bridges: I:G.78 Salt bridges: I:R.19 48P.10: 12 residues within 4Å: Chain J: R.19, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 Chain K: D.88 11 PLIP interactions: 11 interactions with chain J Hydrophobic interactions: J:V.105 Hydrogen bonds: J:R.19, J:N.75, J:H.81, J:H.101, J:I.102, J:S.103, J:R.108, J:R.112 Water bridges: J:G.78 Salt bridges: J:R.19 48P.11: 12 residues within 4Å: Chain A: D.88 Chain K: R.19, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 12 PLIP interactions: 11 interactions with chain K, 1 interactions with chain A Hydrophobic interactions: K:V.105 Hydrogen bonds: K:R.19, K:N.75, K:H.81, K:H.101, K:I.102, K:S.103, K:R.108, K:R.112, A:D.88 Water bridges: K:G.78 Salt bridges: K:R.19 48P.12: 12 residues within 4Å: Chain I: D.88 Chain L: R.19, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 11 PLIP interactions: 11 interactions with chain L Hydrophobic interactions: L:V.105 Hydrogen bonds: L:R.19, L:N.75, L:H.81, L:H.101, L:I.102, L:S.103, L:R.108, L:R.112 Water bridges: L:G.78 Salt bridges: L:R.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blanco, B. et al., Exploring the water-binding pocket of the type II dehydroquinase enzyme in the structure-based design of inhibitors. J. Med. Chem. (2014)

Release Date

2014-04-16

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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