SMTL ID : 3n8k.2 (1 other biounit)

Type II dehydroquinase from Mycobacterium tuberculosis complexed with citrazinic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-12-mer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: H.132, V.150 Chain G: H.132 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain B: H.132, V.150 Chain F: H.132 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain C: H.132 Chain H: H.132, V.150 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain D: H.132, V.150 Chain I: H.132 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain E: H.132 Chain K: H.132, V.150 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain G: G.40, R.41 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain J: H.132, V.150 Chain L: H.132, V.152 Ligand excluded by PLIP

10 x D1X: 2,6-dioxo-1,2,3,6-tetrahydropyridine-4-carboxylic acid(Non-covalent)

D1X.2: 13 residues within 4Å: Chain A: P.37, R.45, Y.50, N.101, G.103, G.104, H.107, H.127, I.128, S.129, V.131, R.138 Chain L: D.114 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain L Hydrophobic interactions: A:Y.50 Hydrogen bonds: A:R.45, A:R.45, A:N.101, A:N.101, A:I.128, A:S.129, A:R.138, L:D.114, L:D.114 Water bridges: A:G.104, A:G.104 Salt bridges: A:H.127 D1X.3: 11 residues within 4Å: Chain B: P.37, R.45, Y.50, N.101, G.103, G.104, H.107, H.127, I.128, S.129, R.138 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.50 Hydrogen bonds: B:R.45, B:R.45, B:Y.50, B:N.101, B:N.101, B:I.128, B:S.129, B:R.138 Water bridges: B:G.104, B:G.104 Salt bridges: B:H.127 D1X.5: 12 residues within 4Å: Chain B: D.114 Chain C: R.45, Y.50, N.101, G.103, G.104, H.107, H.127, I.128, S.129, V.131, R.138 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:Y.50, C:V.131 Hydrogen bonds: C:R.45, C:R.45, C:N.101, C:N.101, C:I.128, C:S.129, C:R.138, B:D.114, B:D.114 Water bridges: C:G.104, C:G.104 Salt bridges: C:H.127 pi-Cation interactions: C:R.134 D1X.7: 13 residues within 4Å: Chain D: P.37, R.45, Y.50, N.101, G.103, G.104, H.107, H.127, I.128, S.129, R.134, R.138 Chain G: D.114 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain G Hydrophobic interactions: D:Y.50 Hydrogen bonds: D:R.45, D:R.45, D:Y.50, D:N.101, D:N.101, D:G.104, D:I.128, D:S.129, D:R.138, G:D.114 Salt bridges: D:H.127 D1X.10: 12 residues within 4Å: Chain D: D.114 Chain F: P.37, R.45, Y.50, N.101, G.103, G.104, H.107, H.127, I.128, S.129, R.138 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: F:Y.50 Hydrogen bonds: F:R.45, F:R.45, F:N.101, F:G.104, F:I.128, F:S.129, F:S.129, F:R.138, D:D.114, D:D.114 Salt bridges: F:H.127 D1X.11: 13 residues within 4Å: Chain F: D.114 Chain G: P.37, R.45, Y.50, N.101, G.103, G.104, H.107, H.127, I.128, S.129, R.134, R.138 12 PLIP interactions: 1 interactions with chain F, 11 interactions with chain G Hydrogen bonds: F:D.114, G:R.45, G:R.45, G:Y.50, G:N.101, G:N.101, G:G.104, G:I.128, G:S.129, G:R.138 Hydrophobic interactions: G:Y.50 Salt bridges: G:H.127 D1X.13: 11 residues within 4Å: Chain H: R.45, Y.50, N.101, G.103, H.107, H.127, I.128, S.129, V.131, R.138 Chain J: D.114 14 PLIP interactions: 1 interactions with chain J, 13 interactions with chain H Hydrogen bonds: J:D.114, H:R.45, H:R.45, H:Y.50, H:N.101, H:I.128, H:S.129, H:S.129, H:R.138 Hydrophobic interactions: H:Y.50, H:V.131 Water bridges: H:G.104, H:G.104 Salt bridges: H:H.127 D1X.14: 14 residues within 4Å: Chain H: D.114 Chain I: P.37, R.45, Y.50, N.101, G.103, G.104, H.107, H.127, I.128, S.129, V.131, R.134, R.138 12 PLIP interactions: 1 interactions with chain H, 11 interactions with chain I Hydrogen bonds: H:D.114, I:R.45, I:R.45, I:Y.50, I:N.101, I:G.104, I:I.128, I:S.129, I:S.129, I:R.138 Hydrophobic interactions: I:Y.50 Salt bridges: I:H.127 D1X.15: 11 residues within 4Å: Chain I: D.114 Chain J: R.45, Y.50, N.101, G.103, G.104, H.107, H.127, I.128, S.129, R.138 14 PLIP interactions: 2 interactions with chain I, 12 interactions with chain J Hydrogen bonds: I:D.114, I:D.114, J:R.45, J:R.45, J:N.101, J:I.128, J:S.129, J:S.129, J:R.138 Hydrophobic interactions: J:Y.50 Water bridges: J:G.104, J:G.104 Salt bridges: J:H.127 pi-Cation interactions: J:R.134 D1X.17: 13 residues within 4Å: Chain A: D.114 Chain K: P.37, R.45, Y.50, N.101, G.103, G.104, H.107, H.127, I.128, S.129, R.134, R.138 12 PLIP interactions: 10 interactions with chain K, 2 interactions with chain A Hydrophobic interactions: K:Y.50 Hydrogen bonds: K:R.45, K:R.45, K:N.101, K:G.104, K:I.128, K:S.129, K:S.129, K:R.138, A:D.114, A:D.114 Salt bridges: K:H.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dias, M.V. et al., Structural investigation of inhibitor designs targeting 3-dehydroquinate dehydratase from the shikimate pathway of Mycobacterium tuberculosis. Biochem.J. (2011)

Release Date

2010-07-21

Peptides

3-dehydroquinate dehydratase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
N

C
O

D
P

E
Q

F
R

G
S

H
T

I
U

J
V

K
W

L
X

3-dehydroquinate dehydratase

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