SMTL ID : 4v0s.1

Crystal structure of Mycobacterium tuberculosis Type II Dehydroquinase D88N mutant inhibited by a 3-dehydroquinic acid derivative

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

3 x 2HN: (1R,2S,4S,5R)-2-(2,3,4,5,6-pentafluorophenyl)methyl-1,4,5-trihydroxy-3-oxocyclohexane-1-carboxylic acid(Non-covalent)

2HN.1: 14 residues within 4Å: Chain A: P.11, N.12, L.13, R.15, L.16, R.19, Y.24, N.75, G.77, G.78, H.101, I.102, S.103, V.105 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.24, A:V.105 Hydrogen bonds: A:N.12, A:N.75, A:N.75, A:N.75, A:G.77, A:I.102, A:S.103 Water bridges: A:N.12, A:G.77, A:H.81 Salt bridges: A:H.101 pi-Stacking: A:Y.24 2HN.2: 8 residues within 4Å: Chain A: N.6, I.8, V.48, R.50, W.61, Q.64, A.65, E.70 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.64, A:Q.64 Water bridges: A:Q.57, A:W.61 Salt bridges: A:R.50 2HN.6: 15 residues within 4Å: Chain B: P.11, N.12, L.13, R.15, L.16, R.19, Y.24, N.75, G.77, G.78, H.101, I.102, S.103, V.105, R.108 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.24, B:V.105 Hydrogen bonds: B:N.12, B:N.75, B:N.75, B:N.75, B:G.77, B:T.80, B:H.101, B:I.102, B:S.103, B:R.108, B:R.108 Water bridges: B:H.81 Salt bridges: B:H.101 pi-Stacking: B:Y.24 Halogen bonds: B:R.19

1 x 7HN: 3,4-DIHYDROXY-2-[(2,3,4,5,6-PENTAFLUOROPHENYL)METHYL]BENZOIC ACID(Non-covalent)

7HN.3: 3 residues within 4Å: Chain A: R.87, N.88, A.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.87 pi-Cation interactions: A:R.87

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

CL.4: 4 residues within 4Å: Chain A: Q.131, L.134, L.135, R.138 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain B: E.39, Q.131, L.135, R.138 Ligand excluded by PLIP

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

NA.5: 2 residues within 4Å: Chain A: E.39, E.42 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.42

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

2016-01-13

Peptides

3-DEHYDROQUINATE DEHYDRATASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3-DEHYDROQUINATE DEHYDRATASE

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