SMTL ID : 1h0s.1

3-dehydroquinate dehydratase from Mycobacterium tuberculosis in complex with 3-hydroxyimino-quinic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-12-mer

Ligands

12 x FA6: 3-HYDROXYIMINO QUINIC ACID(Non-covalent)

FA6.1: 14 residues within 4Å: Chain A: P.11, N.12, L.13, R.19, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain C: D.88 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:V.105 Hydrogen bonds: A:P.11, A:R.19, A:N.75, A:N.75, A:G.77, A:G.78, A:I.102, A:S.103, A:S.103, A:R.112, C:D.88, C:D.88 Water bridges: A:N.12 Salt bridges: A:H.101 FA6.8: 14 residues within 4Å: Chain B: P.11, N.12, L.13, R.19, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain D: D.88 14 PLIP interactions: 1 interactions with chain D, 13 interactions with chain B Hydrogen bonds: D:D.88, B:P.11, B:R.19, B:N.75, B:N.75, B:G.77, B:G.78, B:I.102, B:S.103, B:S.103, B:R.112 Hydrophobic interactions: B:V.105 Water bridges: B:N.12 Salt bridges: B:H.101 FA6.15: 14 residues within 4Å: Chain C: P.11, N.12, L.13, R.19, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain J: D.88 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:V.105 Hydrogen bonds: C:P.11, C:R.19, C:N.75, C:N.75, C:G.77, C:G.78, C:I.102, C:S.103, C:S.103, C:R.112, J:D.88 Water bridges: C:N.12 Salt bridges: C:H.101 FA6.22: 14 residues within 4Å: Chain D: P.11, N.12, L.13, R.19, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain I: D.88 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain I Hydrophobic interactions: D:V.105 Hydrogen bonds: D:P.11, D:R.19, D:N.75, D:N.75, D:G.77, D:G.78, D:I.102, D:S.103, D:S.103, D:R.112, I:D.88, I:D.88 Water bridges: D:N.12 Salt bridges: D:H.101 FA6.29: 14 residues within 4Å: Chain E: P.11, N.12, L.13, R.19, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain G: D.88 16 PLIP interactions: 14 interactions with chain E, 2 interactions with chain G Hydrophobic interactions: E:V.105 Hydrogen bonds: E:P.11, E:R.19, E:N.75, E:N.75, E:G.77, E:G.78, E:H.101, E:I.102, E:S.103, E:S.103, E:R.112, G:D.88, G:D.88 Water bridges: E:N.12 Salt bridges: E:H.101 FA6.36: 14 residues within 4Å: Chain F: P.11, N.12, L.13, R.19, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain H: D.88 16 PLIP interactions: 14 interactions with chain F, 2 interactions with chain H Hydrophobic interactions: F:V.105 Hydrogen bonds: F:P.11, F:R.19, F:N.75, F:N.75, F:G.77, F:G.78, F:H.101, F:I.102, F:S.103, F:S.103, F:R.112, H:D.88, H:D.88 Water bridges: F:N.12 Salt bridges: F:H.101 FA6.43: 14 residues within 4Å: Chain G: P.11, N.12, L.13, R.19, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain K: D.88 15 PLIP interactions: 14 interactions with chain G, 1 interactions with chain K Hydrophobic interactions: G:V.105 Hydrogen bonds: G:P.11, G:R.19, G:N.75, G:N.75, G:G.77, G:G.78, G:H.101, G:I.102, G:S.103, G:S.103, G:R.112, K:D.88 Water bridges: G:N.12 Salt bridges: G:H.101 FA6.50: 14 residues within 4Å: Chain H: P.11, N.12, L.13, R.19, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain L: D.88 15 PLIP interactions: 14 interactions with chain H, 1 interactions with chain L Hydrophobic interactions: H:V.105 Hydrogen bonds: H:P.11, H:R.19, H:N.75, H:N.75, H:G.77, H:G.78, H:H.101, H:I.102, H:S.103, H:S.103, H:R.112, L:D.88 Water bridges: H:N.12 Salt bridges: H:H.101 FA6.57: 14 residues within 4Å: Chain B: D.88 Chain I: P.11, N.12, L.13, R.19, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 14 PLIP interactions: 13 interactions with chain I, 1 interactions with chain B Hydrophobic interactions: I:V.105 Hydrogen bonds: I:P.11, I:R.19, I:N.75, I:N.75, I:G.77, I:G.78, I:I.102, I:S.103, I:S.103, I:R.112, B:D.88 Water bridges: I:N.12 Salt bridges: I:H.101 FA6.64: 14 residues within 4Å: Chain A: D.88 Chain J: P.11, N.12, L.13, R.19, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 14 PLIP interactions: 13 interactions with chain J, 1 interactions with chain A Hydrophobic interactions: J:V.105 Hydrogen bonds: J:P.11, J:R.19, J:N.75, J:N.75, J:G.77, J:G.78, J:I.102, J:S.103, J:S.103, J:R.112, A:D.88 Water bridges: J:N.12 Salt bridges: J:H.101 FA6.71: 14 residues within 4Å: Chain E: D.88 Chain K: P.11, N.12, L.13, R.19, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 16 PLIP interactions: 2 interactions with chain E, 14 interactions with chain K Hydrogen bonds: E:D.88, E:D.88, K:P.11, K:R.19, K:N.75, K:N.75, K:G.77, K:G.78, K:H.101, K:I.102, K:S.103, K:S.103, K:R.112 Hydrophobic interactions: K:V.105 Water bridges: K:N.12 Salt bridges: K:H.101 FA6.78: 14 residues within 4Å: Chain F: D.88 Chain L: P.11, N.12, L.13, R.19, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 16 PLIP interactions: 14 interactions with chain L, 2 interactions with chain F Hydrophobic interactions: L:V.105 Hydrogen bonds: L:P.11, L:R.19, L:N.75, L:N.75, L:G.77, L:G.78, L:H.101, L:I.102, L:S.103, L:S.103, L:R.112, F:D.88, F:D.88 Water bridges: L:N.12 Salt bridges: L:H.101

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

SO4.2: 8 residues within 4Å: Chain A: S.54, A.56 Chain C: S.54, A.56 Chain J: S.54, A.56 Ligands: SO4.16, SO4.65 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: R.87, P.119 Chain J: E.109, F.111 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.9: 8 residues within 4Å: Chain B: S.54, A.56 Chain D: S.54, A.56 Chain I: S.54, A.56 Ligands: SO4.23, SO4.58 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain B: R.87, P.119 Chain I: E.109, F.111 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain B: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.16: 8 residues within 4Å: Chain A: S.54, A.56 Chain C: S.54, A.56 Chain J: S.54, A.56 Ligands: SO4.2, SO4.65 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain A: E.109, F.111 Chain C: R.87, P.119 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain C: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.23: 8 residues within 4Å: Chain B: S.54, A.56 Chain D: S.54, A.56 Chain I: S.54, A.56 Ligands: SO4.9, SO4.58 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain B: E.109, F.111 Chain D: R.87, P.119 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain D: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.30: 8 residues within 4Å: Chain E: S.54, A.56 Chain G: S.54, A.56 Chain K: S.54, A.56 Ligands: SO4.44, SO4.72 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain E: R.87, P.119 Chain K: E.109, F.111 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain E: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.37: 8 residues within 4Å: Chain F: S.54, A.56 Chain H: S.54, A.56 Chain L: S.54, A.56 Ligands: SO4.51, SO4.79 Ligand excluded by PLIP SO4.38: 4 residues within 4Å: Chain F: R.87, P.119 Chain L: E.109, F.111 Ligand excluded by PLIP SO4.39: 3 residues within 4Å: Chain F: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.44: 8 residues within 4Å: Chain E: S.54, A.56 Chain G: S.54, A.56 Chain K: S.54, A.56 Ligands: SO4.30, SO4.72 Ligand excluded by PLIP SO4.45: 4 residues within 4Å: Chain E: E.109, F.111 Chain G: R.87, P.119 Ligand excluded by PLIP SO4.46: 3 residues within 4Å: Chain G: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.51: 8 residues within 4Å: Chain F: S.54, A.56 Chain H: S.54, A.56 Chain L: S.54, A.56 Ligands: SO4.37, SO4.79 Ligand excluded by PLIP SO4.52: 4 residues within 4Å: Chain F: E.109, F.111 Chain H: R.87, P.119 Ligand excluded by PLIP SO4.53: 3 residues within 4Å: Chain H: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.58: 8 residues within 4Å: Chain B: S.54, A.56 Chain D: S.54, A.56 Chain I: S.54, A.56 Ligands: SO4.9, SO4.23 Ligand excluded by PLIP SO4.59: 4 residues within 4Å: Chain D: E.109, F.111 Chain I: R.87, P.119 Ligand excluded by PLIP SO4.60: 3 residues within 4Å: Chain I: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.65: 8 residues within 4Å: Chain A: S.54, A.56 Chain C: S.54, A.56 Chain J: S.54, A.56 Ligands: SO4.2, SO4.16 Ligand excluded by PLIP SO4.66: 4 residues within 4Å: Chain C: E.109, F.111 Chain J: R.87, P.119 Ligand excluded by PLIP SO4.67: 3 residues within 4Å: Chain J: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.72: 8 residues within 4Å: Chain E: S.54, A.56 Chain G: S.54, A.56 Chain K: S.54, A.56 Ligands: SO4.30, SO4.44 Ligand excluded by PLIP SO4.73: 4 residues within 4Å: Chain G: E.109, F.111 Chain K: R.87, P.119 Ligand excluded by PLIP SO4.74: 3 residues within 4Å: Chain K: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.79: 8 residues within 4Å: Chain F: S.54, A.56 Chain H: S.54, A.56 Chain L: S.54, A.56 Ligands: SO4.37, SO4.51 Ligand excluded by PLIP SO4.80: 4 residues within 4Å: Chain H: E.109, F.111 Chain L: R.87, P.119 Ligand excluded by PLIP SO4.81: 3 residues within 4Å: Chain L: R.50, W.61, Q.64 Ligand excluded by PLIP

36 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP GOL.6: 4 residues within 4Å: Chain A: H.81, H.114, S.115, Y.116 Ligand excluded by PLIP GOL.7: 4 residues within 4Å: Chain A: K.46, A.47, V.48, R.50 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain B: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain B: H.81, H.114, S.115, Y.116 Ligand excluded by PLIP GOL.14: 4 residues within 4Å: Chain B: K.46, A.47, V.48, R.50 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain C: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain C: H.81, H.114, S.115, Y.116 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain C: K.46, A.47, V.48, R.50 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain D: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain D: H.81, H.114, S.115, Y.116 Ligand excluded by PLIP GOL.28: 4 residues within 4Å: Chain D: K.46, A.47, V.48, R.50 Ligand excluded by PLIP GOL.33: 4 residues within 4Å: Chain E: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP GOL.34: 4 residues within 4Å: Chain E: H.81, H.114, S.115, Y.116 Ligand excluded by PLIP GOL.35: 4 residues within 4Å: Chain E: K.46, A.47, V.48, R.50 Ligand excluded by PLIP GOL.40: 4 residues within 4Å: Chain F: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP GOL.41: 4 residues within 4Å: Chain F: H.81, H.114, S.115, Y.116 Ligand excluded by PLIP GOL.42: 4 residues within 4Å: Chain F: K.46, A.47, V.48, R.50 Ligand excluded by PLIP GOL.47: 4 residues within 4Å: Chain G: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP GOL.48: 4 residues within 4Å: Chain G: H.81, H.114, S.115, Y.116 Ligand excluded by PLIP GOL.49: 4 residues within 4Å: Chain G: K.46, A.47, V.48, R.50 Ligand excluded by PLIP GOL.54: 4 residues within 4Å: Chain H: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP GOL.55: 4 residues within 4Å: Chain H: H.81, H.114, S.115, Y.116 Ligand excluded by PLIP GOL.56: 4 residues within 4Å: Chain H: K.46, A.47, V.48, R.50 Ligand excluded by PLIP GOL.61: 4 residues within 4Å: Chain I: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP GOL.62: 4 residues within 4Å: Chain I: H.81, H.114, S.115, Y.116 Ligand excluded by PLIP GOL.63: 4 residues within 4Å: Chain I: K.46, A.47, V.48, R.50 Ligand excluded by PLIP GOL.68: 4 residues within 4Å: Chain J: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP GOL.69: 4 residues within 4Å: Chain J: H.81, H.114, S.115, Y.116 Ligand excluded by PLIP GOL.70: 4 residues within 4Å: Chain J: K.46, A.47, V.48, R.50 Ligand excluded by PLIP GOL.75: 4 residues within 4Å: Chain K: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP GOL.76: 4 residues within 4Å: Chain K: H.81, H.114, S.115, Y.116 Ligand excluded by PLIP GOL.77: 4 residues within 4Å: Chain K: K.46, A.47, V.48, R.50 Ligand excluded by PLIP GOL.82: 4 residues within 4Å: Chain L: L.128, G.129, I.130, Q.131 Ligand excluded by PLIP GOL.83: 4 residues within 4Å: Chain L: H.81, H.114, S.115, Y.116 Ligand excluded by PLIP GOL.84: 4 residues within 4Å: Chain L: K.46, A.47, V.48, R.50 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Robinson, D.A. et al., Structural Basis for Specificity of Oxime Based Inhibitors Towards Type II Dehydroquinase from Mycobacterium Tuberculosis. To be Published

Release Date

2003-07-17

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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