SMTL ID : 4ciw.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-12-mer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: S.54 Chain E: S.54 Chain I: S.54 Ligands: SO4.21, SO4.41 10 PLIP interactions: 3 interactions with chain I, 4 interactions with chain E, 3 interactions with chain A Hydrogen bonds: I:S.54, E:S.54 Water bridges: I:A.56, I:Q.57, E:S.54, E:A.56, E:Q.57, A:A.56, A:A.56, A:Q.57 SO4.6: 5 residues within 4Å: Chain B: S.54 Chain F: S.54 Chain L: S.54 Ligands: SO4.26, SO4.56 10 PLIP interactions: 3 interactions with chain L, 3 interactions with chain B, 4 interactions with chain F Hydrogen bonds: L:S.54, F:S.54 Water bridges: L:A.56, L:Q.57, B:A.56, B:A.56, B:Q.57, F:S.54, F:A.56, F:Q.57 SO4.11: 5 residues within 4Å: Chain C: S.54 Chain H: S.54 Chain K: S.54 Ligands: SO4.36, SO4.51 10 PLIP interactions: 4 interactions with chain C, 3 interactions with chain H, 3 interactions with chain K Water bridges: C:S.54, C:A.56, C:A.56, C:Q.57, H:A.56, H:Q.57, K:S.54, K:A.56, K:Q.57 Hydrogen bonds: H:S.54 SO4.16: 5 residues within 4Å: Chain D: S.54 Chain G: S.54 Chain J: S.54 Ligands: SO4.31, SO4.46 10 PLIP interactions: 3 interactions with chain G, 3 interactions with chain J, 4 interactions with chain D Hydrogen bonds: G:S.54 Water bridges: G:A.56, G:Q.57, J:S.54, J:A.56, J:Q.57, D:S.54, D:A.56, D:A.56, D:Q.57 SO4.21: 5 residues within 4Å: Chain A: S.54 Chain E: S.54 Chain I: S.54 Ligands: SO4.1, SO4.41 10 PLIP interactions: 3 interactions with chain I, 4 interactions with chain E, 3 interactions with chain A Water bridges: I:S.54, I:A.56, I:Q.57, E:S.54, E:A.56, E:A.56, E:Q.57, A:A.56, A:Q.57 Hydrogen bonds: A:S.54 SO4.26: 5 residues within 4Å: Chain B: S.54 Chain F: S.54 Chain L: S.54 Ligands: SO4.6, SO4.56 10 PLIP interactions: 3 interactions with chain L, 3 interactions with chain B, 4 interactions with chain F Water bridges: L:S.54, L:A.56, L:Q.57, B:A.56, B:Q.57, F:S.54, F:A.56, F:A.56, F:Q.57 Hydrogen bonds: B:S.54 SO4.31: 5 residues within 4Å: Chain D: S.54 Chain G: S.54 Chain J: S.54 Ligands: SO4.16, SO4.46 10 PLIP interactions: 3 interactions with chain J, 4 interactions with chain D, 3 interactions with chain G Hydrogen bonds: J:S.54, D:S.54 Water bridges: J:A.56, J:Q.57, D:S.54, D:A.56, D:Q.57, G:A.56, G:A.56, G:Q.57 SO4.36: 5 residues within 4Å: Chain C: S.54 Chain H: S.54 Chain K: S.54 Ligands: SO4.11, SO4.51 10 PLIP interactions: 4 interactions with chain C, 3 interactions with chain H, 3 interactions with chain K Hydrogen bonds: C:S.54, K:S.54 Water bridges: C:S.54, C:A.56, C:Q.57, H:A.56, H:A.56, H:Q.57, K:A.56, K:Q.57 SO4.41: 5 residues within 4Å: Chain A: S.54 Chain E: S.54 Chain I: S.54 Ligands: SO4.1, SO4.21 11 PLIP interactions: 3 interactions with chain E, 4 interactions with chain A, 4 interactions with chain I Hydrogen bonds: E:S.54, A:S.54 Water bridges: E:A.56, E:Q.57, A:S.54, A:A.56, A:Q.57, I:S.54, I:A.56, I:A.56, I:Q.57 SO4.46: 5 residues within 4Å: Chain D: S.54 Chain G: S.54 Chain J: S.54 Ligands: SO4.16, SO4.31 11 PLIP interactions: 4 interactions with chain J, 3 interactions with chain D, 4 interactions with chain G Water bridges: J:S.54, J:A.56, J:A.56, J:Q.57, D:A.56, D:Q.57, G:S.54, G:A.56, G:Q.57 Hydrogen bonds: D:S.54, G:S.54 SO4.51: 5 residues within 4Å: Chain C: S.54 Chain H: S.54 Chain K: S.54 Ligands: SO4.11, SO4.36 11 PLIP interactions: 4 interactions with chain H, 4 interactions with chain K, 3 interactions with chain C Hydrogen bonds: H:S.54, C:S.54 Water bridges: H:S.54, H:A.56, H:Q.57, K:S.54, K:A.56, K:A.56, K:Q.57, C:A.56, C:Q.57 SO4.56: 5 residues within 4Å: Chain B: S.54 Chain F: S.54 Chain L: S.54 Ligands: SO4.6, SO4.26 11 PLIP interactions: 3 interactions with chain F, 4 interactions with chain L, 4 interactions with chain B Hydrogen bonds: F:S.54, B:S.54 Water bridges: F:A.56, F:Q.57, L:S.54, L:A.56, L:A.56, L:Q.57, B:S.54, B:A.56, B:Q.57

36 x NA: SODIUM ION(Non-functional Binders)

NA.2: 4 residues within 4Å: Chain A: I.4, N.6, V.48, E.70 Ligand excluded by PLIP NA.3: 4 residues within 4Å: Chain A: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP NA.4: 4 residues within 4Å: Chain A: R.87, H.114, P.119 Chain D: R.113 Ligand excluded by PLIP NA.7: 4 residues within 4Å: Chain B: I.4, N.6, V.48, E.70 Ligand excluded by PLIP NA.8: 4 residues within 4Å: Chain B: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP NA.9: 4 residues within 4Å: Chain B: R.87, H.114, P.119 Chain I: R.113 Ligand excluded by PLIP NA.12: 4 residues within 4Å: Chain C: I.4, N.6, V.48, E.70 Ligand excluded by PLIP NA.13: 4 residues within 4Å: Chain C: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP NA.14: 4 residues within 4Å: Chain C: R.87, H.114, P.119 Chain E: R.113 Ligand excluded by PLIP NA.17: 4 residues within 4Å: Chain D: I.4, N.6, V.48, E.70 Ligand excluded by PLIP NA.18: 4 residues within 4Å: Chain D: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP NA.19: 4 residues within 4Å: Chain A: R.113 Chain D: R.87, H.114, P.119 Ligand excluded by PLIP NA.22: 4 residues within 4Å: Chain E: I.4, N.6, V.48, E.70 Ligand excluded by PLIP NA.23: 4 residues within 4Å: Chain E: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP NA.24: 4 residues within 4Å: Chain C: R.113 Chain E: R.87, H.114, P.119 Ligand excluded by PLIP NA.27: 4 residues within 4Å: Chain F: I.4, N.6, V.48, E.70 Ligand excluded by PLIP NA.28: 4 residues within 4Å: Chain F: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP NA.29: 4 residues within 4Å: Chain F: R.87, H.114, P.119 Chain H: R.113 Ligand excluded by PLIP NA.32: 4 residues within 4Å: Chain G: I.4, N.6, V.48, E.70 Ligand excluded by PLIP NA.33: 4 residues within 4Å: Chain G: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP NA.34: 4 residues within 4Å: Chain G: R.87, H.114, P.119 Chain K: R.113 Ligand excluded by PLIP NA.37: 4 residues within 4Å: Chain H: I.4, N.6, V.48, E.70 Ligand excluded by PLIP NA.38: 4 residues within 4Å: Chain H: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP NA.39: 4 residues within 4Å: Chain F: R.113 Chain H: R.87, H.114, P.119 Ligand excluded by PLIP NA.42: 4 residues within 4Å: Chain I: I.4, N.6, V.48, E.70 Ligand excluded by PLIP NA.43: 4 residues within 4Å: Chain I: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP NA.44: 4 residues within 4Å: Chain B: R.113 Chain I: R.87, H.114, P.119 Ligand excluded by PLIP NA.47: 4 residues within 4Å: Chain J: I.4, N.6, V.48, E.70 Ligand excluded by PLIP NA.48: 4 residues within 4Å: Chain J: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP NA.49: 4 residues within 4Å: Chain J: R.87, H.114, P.119 Chain L: R.113 Ligand excluded by PLIP NA.52: 4 residues within 4Å: Chain K: I.4, N.6, V.48, E.70 Ligand excluded by PLIP NA.53: 4 residues within 4Å: Chain K: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP NA.54: 4 residues within 4Å: Chain G: R.113 Chain K: R.87, H.114, P.119 Ligand excluded by PLIP NA.57: 4 residues within 4Å: Chain L: I.4, N.6, V.48, E.70 Ligand excluded by PLIP NA.58: 4 residues within 4Å: Chain L: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP NA.59: 4 residues within 4Å: Chain J: R.113 Chain L: R.87, H.114, P.119 Ligand excluded by PLIP

12 x XH2: (1R,4R,5R)-1,4,5-trihydroxy-3-(2-hydroxy)ethylcyclohex-2-ene-1-carboxylic acid(Non-covalent)

XH2.5: 12 residues within 4Å: Chain A: N.12, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain I: D.88 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: A:Y.24, A:V.105 Hydrogen bonds: A:N.75, A:G.77, A:H.81, A:H.101, A:I.102, A:S.103, A:S.103, A:R.112, I:D.88 Water bridges: A:G.78 Salt bridges: A:H.101 XH2.10: 12 residues within 4Å: Chain B: N.12, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain L: D.88 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.24, B:V.105 Hydrogen bonds: B:N.75, B:G.77, B:H.81, B:H.101, B:I.102, B:S.103, B:S.103, B:R.112 Water bridges: B:G.78 Salt bridges: B:H.101 XH2.15: 12 residues within 4Å: Chain C: N.12, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain H: D.88 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain H Hydrophobic interactions: C:Y.24, C:V.105 Hydrogen bonds: C:N.75, C:G.77, C:H.81, C:H.101, C:I.102, C:S.103, C:S.103, C:R.112, H:D.88 Water bridges: C:G.78 Salt bridges: C:H.101 XH2.20: 12 residues within 4Å: Chain D: N.12, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain G: D.88 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain G Hydrophobic interactions: D:Y.24, D:V.105 Hydrogen bonds: D:N.75, D:G.77, D:H.81, D:H.101, D:I.102, D:S.103, D:S.103, D:R.112, G:D.88 Water bridges: D:G.78 Salt bridges: D:H.101 XH2.25: 12 residues within 4Å: Chain A: D.88 Chain E: N.12, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:Y.24, E:V.105 Hydrogen bonds: E:N.75, E:G.77, E:H.81, E:H.101, E:I.102, E:S.103, E:S.103, E:R.112 Water bridges: E:G.78 Salt bridges: E:H.101 XH2.30: 12 residues within 4Å: Chain B: D.88 Chain F: N.12, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:Y.24, F:V.105 Hydrogen bonds: F:N.75, F:G.77, F:H.81, F:H.101, F:I.102, F:S.103, F:S.103, F:R.112 Water bridges: F:G.78 Salt bridges: F:H.101 XH2.35: 12 residues within 4Å: Chain G: N.12, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain J: D.88 13 PLIP interactions: 12 interactions with chain G, 1 interactions with chain J Hydrophobic interactions: G:Y.24, G:V.105 Hydrogen bonds: G:N.75, G:G.77, G:H.81, G:H.101, G:I.102, G:S.103, G:S.103, G:R.112, J:D.88 Water bridges: G:G.78 Salt bridges: G:H.101 XH2.40: 12 residues within 4Å: Chain H: N.12, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain K: D.88 12 PLIP interactions: 12 interactions with chain H Hydrophobic interactions: H:Y.24, H:V.105 Hydrogen bonds: H:N.75, H:G.77, H:H.81, H:H.101, H:I.102, H:S.103, H:S.103, H:R.112 Water bridges: H:G.78 Salt bridges: H:H.101 XH2.45: 12 residues within 4Å: Chain E: D.88 Chain I: N.12, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 13 PLIP interactions: 12 interactions with chain I, 1 interactions with chain E Hydrophobic interactions: I:Y.24, I:V.105 Hydrogen bonds: I:N.75, I:G.77, I:H.81, I:H.101, I:I.102, I:S.103, I:S.103, I:R.112, E:D.88 Water bridges: I:G.78 Salt bridges: I:H.101 XH2.50: 12 residues within 4Å: Chain D: D.88 Chain J: N.12, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 12 PLIP interactions: 12 interactions with chain J Hydrophobic interactions: J:Y.24, J:V.105 Hydrogen bonds: J:N.75, J:G.77, J:H.81, J:H.101, J:I.102, J:S.103, J:S.103, J:R.112 Water bridges: J:G.78 Salt bridges: J:H.101 XH2.55: 12 residues within 4Å: Chain C: D.88 Chain K: N.12, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 12 PLIP interactions: 12 interactions with chain K Hydrophobic interactions: K:Y.24, K:V.105 Hydrogen bonds: K:N.75, K:G.77, K:H.81, K:H.101, K:I.102, K:S.103, K:S.103, K:R.112 Water bridges: K:G.78 Salt bridges: K:H.101 XH2.60: 12 residues within 4Å: Chain F: D.88 Chain L: N.12, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 13 PLIP interactions: 12 interactions with chain L, 1 interactions with chain F Hydrophobic interactions: L:Y.24, L:V.105 Hydrogen bonds: L:N.75, L:G.77, L:H.81, L:H.101, L:I.102, L:S.103, L:S.103, L:R.112, F:D.88 Water bridges: L:G.78 Salt bridges: L:H.101

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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