SMTL ID : 4cky.1

Structure of the Mycobacterium tuberculosis Type II Dehydroquinase inhibited by a 3-dehydroquinic acid derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-12-mer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: I.4, N.6, E.70 Ligand excluded by PLIP NA.2: 5 residues within 4Å: Chain A: L.128, G.129, I.130, Q.131 Chain H: H.143 Ligand excluded by PLIP NA.3: 5 residues within 4Å: Chain A: R.87, H.114, S.115, P.119 Chain H: R.113 Ligand excluded by PLIP NA.6: 3 residues within 4Å: Chain B: I.4, N.6, E.70 Ligand excluded by PLIP NA.7: 5 residues within 4Å: Chain B: L.128, G.129, I.130, Q.131 Chain K: H.143 Ligand excluded by PLIP NA.8: 5 residues within 4Å: Chain B: R.87, H.114, S.115, P.119 Chain K: R.113 Ligand excluded by PLIP NA.11: 3 residues within 4Å: Chain C: I.4, N.6, E.70 Ligand excluded by PLIP NA.12: 5 residues within 4Å: Chain C: L.128, G.129, I.130, Q.131 Chain J: H.143 Ligand excluded by PLIP NA.13: 5 residues within 4Å: Chain C: R.87, H.114, S.115, P.119 Chain J: R.113 Ligand excluded by PLIP NA.16: 3 residues within 4Å: Chain D: I.4, N.6, E.70 Ligand excluded by PLIP NA.17: 5 residues within 4Å: Chain D: L.128, G.129, I.130, Q.131 Chain F: H.143 Ligand excluded by PLIP NA.18: 5 residues within 4Å: Chain D: R.87, H.114, S.115, P.119 Chain F: R.113 Ligand excluded by PLIP NA.21: 3 residues within 4Å: Chain E: I.4, N.6, E.70 Ligand excluded by PLIP NA.22: 5 residues within 4Å: Chain E: L.128, G.129, I.130, Q.131 Chain L: H.143 Ligand excluded by PLIP NA.23: 5 residues within 4Å: Chain E: R.87, H.114, S.115, P.119 Chain L: R.113 Ligand excluded by PLIP NA.26: 3 residues within 4Å: Chain F: I.4, N.6, E.70 Ligand excluded by PLIP NA.27: 5 residues within 4Å: Chain D: H.143 Chain F: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP NA.28: 5 residues within 4Å: Chain D: R.113 Chain F: R.87, H.114, S.115, P.119 Ligand excluded by PLIP NA.31: 3 residues within 4Å: Chain G: I.4, N.6, E.70 Ligand excluded by PLIP NA.32: 5 residues within 4Å: Chain G: L.128, G.129, I.130, Q.131 Chain I: H.143 Ligand excluded by PLIP NA.33: 5 residues within 4Å: Chain G: R.87, H.114, S.115, P.119 Chain I: R.113 Ligand excluded by PLIP NA.36: 3 residues within 4Å: Chain H: I.4, N.6, E.70 Ligand excluded by PLIP NA.37: 5 residues within 4Å: Chain A: H.143 Chain H: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP NA.38: 5 residues within 4Å: Chain A: R.113 Chain H: R.87, H.114, S.115, P.119 Ligand excluded by PLIP NA.41: 3 residues within 4Å: Chain I: I.4, N.6, E.70 Ligand excluded by PLIP NA.42: 5 residues within 4Å: Chain G: H.143 Chain I: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP NA.43: 5 residues within 4Å: Chain G: R.113 Chain I: R.87, H.114, S.115, P.119 Ligand excluded by PLIP NA.46: 3 residues within 4Å: Chain J: I.4, N.6, E.70 Ligand excluded by PLIP NA.47: 5 residues within 4Å: Chain C: H.143 Chain J: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP NA.48: 5 residues within 4Å: Chain C: R.113 Chain J: R.87, H.114, S.115, P.119 Ligand excluded by PLIP NA.51: 3 residues within 4Å: Chain K: I.4, N.6, E.70 Ligand excluded by PLIP NA.52: 5 residues within 4Å: Chain B: H.143 Chain K: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP NA.53: 5 residues within 4Å: Chain B: R.113 Chain K: R.87, H.114, S.115, P.119 Ligand excluded by PLIP NA.56: 3 residues within 4Å: Chain L: I.4, N.6, E.70 Ligand excluded by PLIP NA.57: 5 residues within 4Å: Chain E: H.143 Chain L: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP NA.58: 5 residues within 4Å: Chain E: R.113 Chain L: R.87, H.114, S.115, P.119 Ligand excluded by PLIP

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

SO4.4: 7 residues within 4Å: Chain A: S.54 Chain K: S.54, A.56 Chain L: S.54, A.56 Ligands: SO4.54, SO4.59 11 PLIP interactions: 4 interactions with chain L, 3 interactions with chain A, 4 interactions with chain K Hydrogen bonds: L:S.54, K:S.54 Water bridges: L:S.54, L:A.56, L:Q.57, A:S.54, A:A.56, A:Q.57, K:S.54, K:S.54, K:A.56 SO4.9: 7 residues within 4Å: Chain B: S.54 Chain C: S.54, A.56 Chain D: S.54, A.56 Ligands: SO4.14, SO4.19 11 PLIP interactions: 3 interactions with chain B, 4 interactions with chain D, 4 interactions with chain C Water bridges: B:S.54, B:A.56, B:Q.57, D:S.54, D:A.56, D:Q.57, C:S.54, C:S.54, C:A.56 Hydrogen bonds: D:S.54, C:S.54 SO4.14: 7 residues within 4Å: Chain B: S.54, A.56 Chain C: S.54 Chain D: S.54, A.56 Ligands: SO4.9, SO4.19 11 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B, 4 interactions with chain D Water bridges: C:S.54, C:A.56, C:Q.57, B:S.54, B:A.56, B:Q.57, D:S.54, D:S.54, D:A.56 Hydrogen bonds: B:S.54, D:S.54 SO4.19: 7 residues within 4Å: Chain B: S.54, A.56 Chain C: S.54, A.56 Chain D: S.54 Ligands: SO4.9, SO4.14 11 PLIP interactions: 4 interactions with chain C, 4 interactions with chain B, 3 interactions with chain D Hydrogen bonds: C:S.54, B:S.54 Water bridges: C:S.54, C:A.56, C:Q.57, B:S.54, B:S.54, B:A.56, D:S.54, D:A.56, D:Q.57 SO4.24: 7 residues within 4Å: Chain E: S.54 Chain F: S.54, A.56 Chain G: S.54, A.56 Ligands: SO4.29, SO4.34 11 PLIP interactions: 4 interactions with chain F, 4 interactions with chain G, 3 interactions with chain E Hydrogen bonds: F:S.54, G:S.54 Water bridges: F:S.54, F:S.54, F:A.56, G:S.54, G:A.56, G:Q.57, E:S.54, E:A.56, E:Q.57 SO4.29: 7 residues within 4Å: Chain E: S.54, A.56 Chain F: S.54 Chain G: S.54, A.56 Ligands: SO4.24, SO4.34 11 PLIP interactions: 3 interactions with chain F, 4 interactions with chain G, 4 interactions with chain E Water bridges: F:S.54, F:A.56, F:Q.57, G:S.54, G:S.54, G:A.56, E:S.54, E:A.56, E:Q.57 Hydrogen bonds: G:S.54, E:S.54 SO4.34: 7 residues within 4Å: Chain E: S.54, A.56 Chain F: S.54, A.56 Chain G: S.54 Ligands: SO4.24, SO4.29 11 PLIP interactions: 4 interactions with chain F, 3 interactions with chain G, 4 interactions with chain E Hydrogen bonds: F:S.54, E:S.54 Water bridges: F:S.54, F:A.56, F:Q.57, G:S.54, G:A.56, G:Q.57, E:S.54, E:S.54, E:A.56 SO4.39: 7 residues within 4Å: Chain H: S.54 Chain I: S.54, A.56 Chain J: S.54, A.56 Ligands: SO4.44, SO4.49 11 PLIP interactions: 4 interactions with chain I, 4 interactions with chain J, 3 interactions with chain H Hydrogen bonds: I:S.54, J:S.54 Water bridges: I:S.54, I:S.54, I:A.56, J:S.54, J:A.56, J:Q.57, H:S.54, H:A.56, H:Q.57 SO4.44: 7 residues within 4Å: Chain H: S.54, A.56 Chain I: S.54 Chain J: S.54, A.56 Ligands: SO4.39, SO4.49 11 PLIP interactions: 4 interactions with chain H, 4 interactions with chain J, 3 interactions with chain I Hydrogen bonds: H:S.54, J:S.54 Water bridges: H:S.54, H:A.56, H:Q.57, J:S.54, J:S.54, J:A.56, I:S.54, I:A.56, I:Q.57 SO4.49: 7 residues within 4Å: Chain H: S.54, A.56 Chain I: S.54, A.56 Chain J: S.54 Ligands: SO4.39, SO4.44 11 PLIP interactions: 4 interactions with chain H, 3 interactions with chain J, 4 interactions with chain I Hydrogen bonds: H:S.54, I:S.54 Water bridges: H:S.54, H:S.54, H:A.56, J:S.54, J:A.56, J:Q.57, I:S.54, I:A.56, I:Q.57 SO4.54: 7 residues within 4Å: Chain A: S.54, A.56 Chain K: S.54 Chain L: S.54, A.56 Ligands: SO4.4, SO4.59 11 PLIP interactions: 3 interactions with chain K, 4 interactions with chain A, 4 interactions with chain L Water bridges: K:S.54, K:A.56, K:Q.57, A:S.54, A:A.56, A:Q.57, L:S.54, L:S.54, L:A.56 Hydrogen bonds: A:S.54, L:S.54 SO4.59: 7 residues within 4Å: Chain A: S.54, A.56 Chain K: S.54, A.56 Chain L: S.54 Ligands: SO4.4, SO4.54 11 PLIP interactions: 4 interactions with chain K, 3 interactions with chain L, 4 interactions with chain A Hydrogen bonds: K:S.54, A:S.54 Water bridges: K:S.54, K:A.56, K:Q.57, L:S.54, L:A.56, L:Q.57, A:S.54, A:S.54, A:A.56

12 x ND3: 2,2-dimethyl-3-dehydroquinic acid(Non-covalent)

ND3.5: 13 residues within 4Å: Chain A: L.13, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 Chain K: V.84, D.88 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.13, A:V.105 Hydrogen bonds: A:N.75, A:N.75, A:G.77, A:H.101, A:I.102, A:S.103, A:R.112 Water bridges: A:G.78, A:G.78 Salt bridges: A:H.101 ND3.10: 13 residues within 4Å: Chain B: L.13, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 Chain C: V.84, D.88 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.13, B:V.105 Hydrogen bonds: B:N.75, B:N.75, B:G.77, B:H.101, B:I.102, B:S.103, B:R.112 Water bridges: B:G.78, C:D.88 Salt bridges: B:H.101 ND3.15: 13 residues within 4Å: Chain C: L.13, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 Chain D: V.84, D.88 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.13, C:V.105 Hydrogen bonds: C:N.75, C:N.75, C:G.77, C:H.101, C:I.102, C:S.103, C:R.112 Water bridges: C:G.78, D:D.88 Salt bridges: C:H.101 ND3.20: 13 residues within 4Å: Chain B: V.84, D.88 Chain D: L.13, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:L.13, D:V.105 Hydrogen bonds: D:N.75, D:N.75, D:G.77, D:H.101, D:I.102, D:S.103, D:R.112 Water bridges: D:G.78, D:G.78 Salt bridges: D:H.101 ND3.25: 13 residues within 4Å: Chain E: L.13, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 Chain F: V.84, D.88 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:L.13, E:V.105 Hydrogen bonds: E:N.75, E:N.75, E:G.77, E:H.101, E:I.102, E:S.103, E:R.112 Water bridges: E:G.78, E:G.78 Salt bridges: E:H.101 ND3.30: 13 residues within 4Å: Chain F: L.13, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 Chain G: V.84, D.88 12 PLIP interactions: 11 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: F:L.13, F:V.105 Hydrogen bonds: F:N.75, F:N.75, F:G.77, F:H.101, F:I.102, F:S.103, F:R.112 Water bridges: F:G.78, G:D.88 Salt bridges: F:H.101 ND3.35: 13 residues within 4Å: Chain E: V.84, D.88 Chain G: L.13, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 12 PLIP interactions: 12 interactions with chain G Hydrophobic interactions: G:L.13, G:V.105 Hydrogen bonds: G:N.75, G:N.75, G:G.77, G:H.101, G:I.102, G:S.103, G:R.112 Water bridges: G:G.78, G:G.78 Salt bridges: G:H.101 ND3.40: 13 residues within 4Å: Chain H: L.13, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 Chain I: V.84, D.88 12 PLIP interactions: 11 interactions with chain H, 1 interactions with chain I Hydrophobic interactions: H:L.13, H:V.105 Hydrogen bonds: H:N.75, H:N.75, H:G.77, H:H.101, H:I.102, H:S.103, H:R.112 Water bridges: H:G.78, I:D.88 Salt bridges: H:H.101 ND3.45: 13 residues within 4Å: Chain I: L.13, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 Chain J: V.84, D.88 12 PLIP interactions: 12 interactions with chain I Hydrophobic interactions: I:L.13, I:V.105 Hydrogen bonds: I:N.75, I:N.75, I:G.77, I:H.101, I:I.102, I:S.103, I:R.112 Water bridges: I:G.78, I:G.78 Salt bridges: I:H.101 ND3.50: 13 residues within 4Å: Chain H: V.84, D.88 Chain J: L.13, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 12 PLIP interactions: 12 interactions with chain J Hydrophobic interactions: J:L.13, J:V.105 Hydrogen bonds: J:N.75, J:N.75, J:G.77, J:H.101, J:I.102, J:S.103, J:R.112 Water bridges: J:G.78, J:G.78 Salt bridges: J:H.101 ND3.55: 13 residues within 4Å: Chain K: L.13, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.108, R.112 Chain L: V.84, D.88 12 PLIP interactions: 11 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: K:L.13, K:V.105 Hydrogen bonds: K:N.75, K:N.75, K:G.77, K:H.101, K:I.102, K:S.103, K:R.112 Water bridges: K:G.78, L:D.88 Salt bridges: K:H.101 ND3.60: 13 residues within 4Å: Chain A: V.84, D.88 Chain L: L.13, 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 L, 1 interactions with chain A Hydrophobic interactions: L:L.13, L:V.105 Hydrogen bonds: L:N.75, L:N.75, L:G.77, L:H.101, L:I.102, L:S.103, L:R.112 Water bridges: L:G.78, A:D.88 Salt bridges: L:H.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maneiro, M. et al., Investigation of the Dehydratation Mechanism Catalyzed by the Type II Dehydroquinase. To be Published

Release Date

2015-03-25

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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