SMTL ID : 4ckx.1

Structure of the Mycobacterium tuberculosis Type II Dehydroquinase N12S mutant (Crystal Form 2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-12-mer

Ligands

12 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 11 residues within 4Å: Chain A: S.54, E.55, A.56 Chain F: S.54, E.55, A.56 Chain J: S.54, E.55, A.56 Ligands: TRS.6, TRS.10 8 PLIP interactions: 2 interactions with chain J, 3 interactions with chain A, 3 interactions with chain F Hydrogen bonds: J:E.55, J:A.56, A:A.56, F:S.54, F:E.55, F:A.56 Water bridges: A:E.55, A:E.55 TRS.2: 11 residues within 4Å: Chain B: S.54, E.55, A.56 Chain D: S.54, E.55, A.56 Chain E: S.54, E.55, A.56 Ligands: TRS.4, TRS.5 7 PLIP interactions: 2 interactions with chain E, 4 interactions with chain D, 1 interactions with chain B Hydrogen bonds: E:E.55, E:A.56, D:S.54, D:E.55, D:A.56, B:A.56 Water bridges: D:E.55 TRS.3: 11 residues within 4Å: Chain C: S.54, E.55, A.56 Chain H: S.54, E.55, A.56 Chain I: S.54, E.55, A.56 Ligands: TRS.8, TRS.9 8 PLIP interactions: 4 interactions with chain I, 2 interactions with chain C, 2 interactions with chain H Hydrogen bonds: I:S.54, I:E.55, I:A.56, C:A.56, H:E.55, H:A.56 Water bridges: I:E.55, C:E.55 TRS.4: 11 residues within 4Å: Chain B: S.54, E.55, A.56 Chain D: S.54, E.55, A.56 Chain E: S.54, E.55, A.56 Ligands: TRS.2, TRS.5 8 PLIP interactions: 3 interactions with chain E, 3 interactions with chain D, 2 interactions with chain B Hydrogen bonds: E:S.54, E:E.55, E:A.56, D:A.56, B:E.55, B:A.56 Water bridges: D:E.55, D:E.55 TRS.5: 11 residues within 4Å: Chain B: S.54, E.55, A.56 Chain D: S.54, E.55, A.56 Chain E: S.54, E.55, A.56 Ligands: TRS.2, TRS.4 8 PLIP interactions: 2 interactions with chain E, 3 interactions with chain D, 3 interactions with chain B Hydrogen bonds: E:A.56, D:E.55, D:A.56, B:S.54, B:E.55, B:A.56 Water bridges: E:E.55, D:E.55 TRS.6: 11 residues within 4Å: Chain A: S.54, E.55, A.56 Chain F: S.54, E.55, A.56 Chain J: S.54, E.55, A.56 Ligands: TRS.1, TRS.10 8 PLIP interactions: 3 interactions with chain J, 3 interactions with chain A, 2 interactions with chain F Hydrogen bonds: J:S.54, J:E.55, J:A.56, A:E.55, A:A.56, F:A.56 Water bridges: A:E.55, F:E.55 TRS.7: 11 residues within 4Å: Chain G: S.54, E.55, A.56 Chain K: S.54, E.55, A.56 Chain L: S.54, E.55, A.56 Ligands: TRS.11, TRS.12 9 PLIP interactions: 3 interactions with chain G, 3 interactions with chain L, 3 interactions with chain K Hydrogen bonds: G:A.56, L:S.54, L:E.55, L:A.56, K:E.55, K:A.56 Water bridges: G:E.55, G:E.55, K:E.55 TRS.8: 11 residues within 4Å: Chain C: S.54, E.55, A.56 Chain H: S.54, E.55, A.56 Chain I: S.54, E.55, A.56 Ligands: TRS.3, TRS.9 8 PLIP interactions: 3 interactions with chain I, 4 interactions with chain C, 1 interactions with chain H Hydrogen bonds: I:E.55, I:A.56, C:S.54, C:E.55, C:A.56, H:A.56 Water bridges: I:E.55, C:E.55 TRS.9: 11 residues within 4Å: Chain C: S.54, E.55, A.56 Chain H: S.54, E.55, A.56 Chain I: S.54, E.55, A.56 Ligands: TRS.3, TRS.8 9 PLIP interactions: 3 interactions with chain I, 3 interactions with chain H, 3 interactions with chain C Hydrogen bonds: I:A.56, H:S.54, H:E.55, H:A.56, C:E.55, C:A.56 Water bridges: I:E.55, I:E.55, C:E.55 TRS.10: 11 residues within 4Å: Chain A: S.54, E.55, A.56 Chain F: S.54, E.55, A.56 Chain J: S.54, E.55, A.56 Ligands: TRS.1, TRS.6 7 PLIP interactions: 4 interactions with chain A, 2 interactions with chain F, 1 interactions with chain J Hydrogen bonds: A:S.54, A:E.55, A:A.56, F:E.55, F:A.56, J:A.56 Water bridges: A:E.55 TRS.11: 11 residues within 4Å: Chain G: S.54, E.55, A.56 Chain K: S.54, E.55, A.56 Chain L: S.54, E.55, A.56 Ligands: TRS.7, TRS.12 8 PLIP interactions: 4 interactions with chain G, 2 interactions with chain L, 2 interactions with chain K Hydrogen bonds: G:S.54, G:E.55, G:A.56, L:E.55, L:A.56, K:A.56 Water bridges: G:E.55, K:E.55 TRS.12: 11 residues within 4Å: Chain G: S.54, E.55, A.56 Chain K: S.54, E.55, A.56 Chain L: S.54, E.55, A.56 Ligands: TRS.7, TRS.11 8 PLIP interactions: 3 interactions with chain G, 1 interactions with chain L, 4 interactions with chain K Hydrogen bonds: G:E.55, G:A.56, L:A.56, K:S.54, K:E.55, K:A.56 Water bridges: G:E.55, K:E.55

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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