SMTL ID : 1h0r.1

Type II Dehydroquinase from Mycobacterium tuberculosis complexed with 2,3-anhydro-quinic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-12-mer

Ligands

12 x FA1: 2,3 -ANHYDRO-QUINIC ACID(Non-covalent)

FA1.1: 11 residues within 4Å: Chain A: Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain C: D.88 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:Y.24, A:V.105 Hydrogen bonds: A:N.75, A:G.77, A:H.81, A:I.102, A:S.103, A:S.103, A:R.112 Water bridges: C:D.88 FA1.6: 11 residues within 4Å: Chain B: Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain G: D.88 11 PLIP interactions: 11 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 FA1.11: 11 residues within 4Å: Chain C: Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain D: D.88 11 PLIP interactions: 11 interactions with chain C 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 Water bridges: C:G.78 FA1.16: 11 residues within 4Å: Chain A: D.88 Chain D: Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:Y.24, D:V.105 Hydrogen bonds: D:N.75, D:G.77, D:H.81, D:I.102, D:S.103, D:S.103, D:R.112 Water bridges: D:G.78 FA1.21: 11 residues within 4Å: Chain E: Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain J: D.88 11 PLIP interactions: 11 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 FA1.26: 11 residues within 4Å: Chain F: Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain K: D.88 11 PLIP interactions: 1 interactions with chain K, 10 interactions with chain F Water bridges: K:D.88 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 FA1.31: 11 residues within 4Å: Chain G: Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain H: D.88 10 PLIP interactions: 9 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: G:Y.24, G:V.105 Hydrogen bonds: G:N.75, G:G.77, G:H.81, G:I.102, G:S.103, G:S.103, G:R.112 Water bridges: H:D.88 FA1.36: 11 residues within 4Å: Chain B: D.88 Chain H: Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 11 PLIP interactions: 10 interactions with chain H, 1 interactions with chain B 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: B:D.88 FA1.41: 11 residues within 4Å: Chain F: D.88 Chain I: Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 10 PLIP interactions: 1 interactions with chain F, 9 interactions with chain I Water bridges: F:D.88 Hydrophobic interactions: I:Y.24, I:V.105 Hydrogen bonds: I:N.75, I:G.77, I:H.81, I:I.102, I:S.103, I:S.103, I:R.112 FA1.46: 11 residues within 4Å: Chain J: Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain L: D.88 10 PLIP interactions: 10 interactions with chain J Hydrophobic interactions: J:Y.24, J:V.105 Hydrogen bonds: J:N.75, J:G.77, J:H.81, J:I.102, J:S.103, J:S.103, J:R.112 Water bridges: J:G.78 FA1.51: 11 residues within 4Å: Chain I: D.88 Chain K: Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 11 PLIP interactions: 11 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 FA1.56: 11 residues within 4Å: Chain E: D.88 Chain L: Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 10 PLIP interactions: 1 interactions with chain E, 9 interactions with chain L Water bridges: E:D.88 Hydrophobic interactions: L:Y.24, L:V.105 Hydrogen bonds: L:N.75, L:G.77, L:H.81, L:I.102, L:S.103, L:S.103, L:R.112

12 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: S.54 Chain C: S.54 Chain D: S.54 Ligands: PO4.12, PO4.17 8 PLIP interactions: 4 interactions with chain D, 3 interactions with chain A, 1 interactions with chain C Water bridges: D:S.54, D:S.54, D:S.54, D:A.56, A:A.56, A:A.56 Hydrogen bonds: A:S.54, C:S.54 PO4.7: 5 residues within 4Å: Chain B: S.54 Chain G: S.54 Chain H: S.54 Ligands: PO4.32, PO4.37 10 PLIP interactions: 5 interactions with chain H, 3 interactions with chain B, 2 interactions with chain G Hydrogen bonds: H:S.54, B:S.54, G:S.54 Water bridges: H:S.54, H:S.54, H:S.54, H:A.56, B:A.56, B:A.56, G:S.54 PO4.12: 5 residues within 4Å: Chain A: S.54 Chain C: S.54 Chain D: S.54 Ligands: PO4.2, PO4.17 9 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C, 2 interactions with chain D Water bridges: A:S.54, A:S.54, A:S.54, A:A.56, C:A.56, C:A.56, D:S.54 Hydrogen bonds: C:S.54, D:S.54 PO4.17: 5 residues within 4Å: Chain A: S.54 Chain C: S.54 Chain D: S.54 Ligands: PO4.2, PO4.12 8 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A, 4 interactions with chain C Hydrogen bonds: D:S.54, A:S.54 Water bridges: D:A.56, D:A.56, C:S.54, C:S.54, C:S.54, C:A.56 PO4.22: 5 residues within 4Å: Chain E: S.54 Chain J: S.54 Chain L: S.54 Ligands: PO4.47, PO4.57 10 PLIP interactions: 5 interactions with chain L, 2 interactions with chain J, 3 interactions with chain E Hydrogen bonds: L:S.54, J:S.54, E:S.54 Water bridges: L:S.54, L:S.54, L:S.54, L:A.56, J:S.54, E:A.56, E:A.56 PO4.27: 5 residues within 4Å: Chain F: S.54 Chain I: S.54 Chain K: S.54 Ligands: PO4.42, PO4.52 9 PLIP interactions: 5 interactions with chain I, 3 interactions with chain F, 1 interactions with chain K Hydrogen bonds: I:S.54, F:S.54, K:S.54 Water bridges: I:S.54, I:S.54, I:S.54, I:A.56, F:A.56, F:A.56 PO4.32: 5 residues within 4Å: Chain B: S.54 Chain G: S.54 Chain H: S.54 Ligands: PO4.7, PO4.37 8 PLIP interactions: 3 interactions with chain G, 1 interactions with chain H, 4 interactions with chain B Hydrogen bonds: G:S.54, H:S.54 Water bridges: G:A.56, G:A.56, B:S.54, B:S.54, B:S.54, B:A.56 PO4.37: 5 residues within 4Å: Chain B: S.54 Chain G: S.54 Chain H: S.54 Ligands: PO4.7, PO4.32 9 PLIP interactions: 5 interactions with chain G, 3 interactions with chain H, 1 interactions with chain B Hydrogen bonds: G:S.54, H:S.54, B:S.54 Water bridges: G:S.54, G:S.54, G:S.54, G:A.56, H:A.56, H:A.56 PO4.42: 5 residues within 4Å: Chain F: S.54 Chain I: S.54 Chain K: S.54 Ligands: PO4.27, PO4.52 8 PLIP interactions: 3 interactions with chain I, 1 interactions with chain F, 4 interactions with chain K Hydrogen bonds: I:S.54, F:S.54 Water bridges: I:A.56, I:A.56, K:S.54, K:S.54, K:S.54, K:A.56 PO4.47: 5 residues within 4Å: Chain E: S.54 Chain J: S.54 Chain L: S.54 Ligands: PO4.22, PO4.57 10 PLIP interactions: 3 interactions with chain J, 5 interactions with chain E, 2 interactions with chain L Hydrogen bonds: J:S.54, E:S.54, L:S.54 Water bridges: J:A.56, J:A.56, E:S.54, E:S.54, E:S.54, E:A.56, L:S.54 PO4.52: 5 residues within 4Å: Chain F: S.54 Chain I: S.54 Chain K: S.54 Ligands: PO4.27, PO4.42 10 PLIP interactions: 5 interactions with chain F, 3 interactions with chain K, 2 interactions with chain I Hydrogen bonds: F:S.54, K:S.54, I:S.54 Water bridges: F:S.54, F:S.54, F:S.54, F:A.56, K:A.56, K:A.56, I:S.54 PO4.57: 5 residues within 4Å: Chain E: S.54 Chain J: S.54 Chain L: S.54 Ligands: PO4.22, PO4.47 10 PLIP interactions: 3 interactions with chain L, 2 interactions with chain E, 5 interactions with chain J Hydrogen bonds: L:S.54, E:S.54, J:S.54 Water bridges: L:A.56, L:A.56, E:S.54, J:S.54, J:S.54, J:S.54, J:A.56

24 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: R.87, H.114, P.119 Chain B: R.113 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: H.106 Chain B: H.106 Ligands: CL.9 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: R.113 Chain B: R.87, H.114, P.119 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: H.106 Chain B: H.106 Ligands: CL.4 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain C: R.87, H.114, P.119 Chain E: R.113 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain C: H.106 Chain E: H.106 Ligands: CL.24 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain D: R.87, H.114, P.119 Chain F: R.113 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain D: H.106 Chain F: H.106 Ligands: CL.29 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain C: R.113 Chain E: R.87, H.114, P.119 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain C: H.106 Chain E: H.106 Ligands: CL.14 Ligand excluded by PLIP CL.28: 4 residues within 4Å: Chain D: R.113 Chain F: R.87, H.114, P.119 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain D: H.106 Chain F: H.106 Ligands: CL.19 Ligand excluded by PLIP CL.33: 4 residues within 4Å: Chain G: R.87, H.114, P.119 Chain I: R.113 Ligand excluded by PLIP CL.34: 3 residues within 4Å: Chain G: H.106 Chain I: H.106 Ligands: CL.44 Ligand excluded by PLIP CL.38: 4 residues within 4Å: Chain H: R.87, H.114, P.119 Chain J: R.113 Ligand excluded by PLIP CL.39: 3 residues within 4Å: Chain H: H.106 Chain J: H.106 Ligands: CL.49 Ligand excluded by PLIP CL.43: 4 residues within 4Å: Chain G: R.113 Chain I: R.87, H.114, P.119 Ligand excluded by PLIP CL.44: 3 residues within 4Å: Chain G: H.106 Chain I: H.106 Ligands: CL.34 Ligand excluded by PLIP CL.48: 4 residues within 4Å: Chain H: R.113 Chain J: R.87, H.114, P.119 Ligand excluded by PLIP CL.49: 3 residues within 4Å: Chain H: H.106 Chain J: H.106 Ligands: CL.39 Ligand excluded by PLIP CL.53: 4 residues within 4Å: Chain K: R.87, H.114, P.119 Chain L: R.113 Ligand excluded by PLIP CL.54: 3 residues within 4Å: Chain K: H.106 Chain L: H.106 Ligands: CL.59 Ligand excluded by PLIP CL.58: 4 residues within 4Å: Chain K: R.113 Chain L: R.87, H.114, P.119 Ligand excluded by PLIP CL.59: 3 residues within 4Å: Chain K: H.106 Chain L: H.106 Ligands: CL.54 Ligand excluded by PLIP

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: R.50, W.61, Q.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.64, A:Q.64 GOL.10: 3 residues within 4Å: Chain B: R.50, W.61, Q.64 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.64, B:Q.64 GOL.15: 3 residues within 4Å: Chain C: R.50, W.61, Q.64 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.64, C:Q.64 GOL.20: 3 residues within 4Å: Chain D: R.50, W.61, Q.64 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.64, D:Q.64 GOL.25: 3 residues within 4Å: Chain E: R.50, W.61, Q.64 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.64, E:Q.64 GOL.30: 3 residues within 4Å: Chain F: R.50, W.61, Q.64 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Q.64, F:Q.64 GOL.35: 3 residues within 4Å: Chain G: R.50, W.61, Q.64 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Q.64, G:Q.64 GOL.40: 3 residues within 4Å: Chain H: R.50, W.61, Q.64 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:Q.64, H:Q.64 GOL.45: 3 residues within 4Å: Chain I: R.50, W.61, Q.64 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:Q.64, I:Q.64 GOL.50: 3 residues within 4Å: Chain J: R.50, W.61, Q.64 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:Q.64, J:Q.64 GOL.55: 3 residues within 4Å: Chain K: R.50, W.61, Q.64 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:Q.64, K:Q.64 GOL.60: 3 residues within 4Å: Chain L: R.50, W.61, Q.64 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:Q.64, L:Q.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2003-10-23

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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