SMTL ID : 3n7a.1 (1 other biounit)

Crystal structure of 3-dehydroquinate dehydratase from Mycobacterium tuberculosis in complex with inhibitor 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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.25, N.76, G.78, G.79, H.82, H.102, I.103, S.104, V.106, R.113 Chain L: D.89 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.25, A:V.106 Hydrogen bonds: A:N.76, A:G.78, A:H.82, A:I.103, A:S.104, A:S.104, A:R.113 Salt bridges: A:H.102 FA1.3: 11 residues within 4Å: Chain B: Y.25, N.76, G.78, G.79, H.82, H.102, I.103, S.104, V.106, R.113 Chain E: D.89 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: B:Y.25, B:V.106 Hydrogen bonds: B:N.76, B:G.78, B:H.82, B:I.103, B:S.104, B:S.104, B:R.113 Water bridges: B:N.13, E:D.89 Salt bridges: B:H.102 FA1.4: 11 residues within 4Å: Chain B: D.89 Chain C: Y.25, N.76, G.78, G.79, H.82, H.102, I.103, S.104, V.106, R.113 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:Y.25, C:V.106 Hydrogen bonds: C:N.76, C:N.76, C:G.78, C:H.82, C:H.102, C:I.103, C:S.104, C:R.113 Water bridges: C:G.79 Salt bridges: C:H.102 FA1.5: 11 residues within 4Å: Chain D: Y.25, N.76, G.78, G.79, H.82, H.102, I.103, S.104, V.106, R.113 Chain G: D.89 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:Y.25, D:V.106 Hydrogen bonds: D:N.76, D:N.76, D:G.78, D:H.82, D:H.102, D:I.103, D:S.104, D:R.109, D:R.113 Water bridges: D:G.79 FA1.7: 11 residues within 4Å: Chain C: D.89 Chain E: Y.25, N.76, G.78, G.79, H.82, H.102, I.103, S.104, V.106, R.113 12 PLIP interactions: 11 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:Y.25, E:V.106 Hydrogen bonds: E:N.76, E:G.78, E:H.82, E:I.103, E:S.104, E:S.104, E:R.113 Water bridges: E:N.13, C:D.89 Salt bridges: E:H.102 FA1.8: 10 residues within 4Å: Chain D: D.89 Chain F: N.76, G.78, G.79, H.82, H.102, I.103, S.104, V.106, R.113 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: F:V.106 Hydrogen bonds: F:N.76, F:G.78, F:H.82, F:H.102, F:I.103, F:S.104, F:S.104, F:R.113 Salt bridges: F:H.102 Water bridges: D:D.89 FA1.10: 11 residues within 4Å: Chain F: D.89 Chain G: Y.25, N.76, G.78, G.79, H.82, H.102, I.103, S.104, V.106, R.113 12 PLIP interactions: 12 interactions with chain G Hydrophobic interactions: G:Y.25, G:V.106 Hydrogen bonds: G:N.76, G:G.78, G:H.82, G:H.102, G:I.103, G:S.104, G:S.104, G:R.113 Water bridges: G:G.79 Salt bridges: G:H.102 FA1.12: 11 residues within 4Å: Chain H: Y.25, N.76, G.78, G.79, H.82, H.102, I.103, S.104, V.106, R.113 Chain J: D.89 11 PLIP interactions: 10 interactions with chain H, 1 interactions with chain J Hydrophobic interactions: H:Y.25, H:V.106 Hydrogen bonds: H:N.76, H:N.76, H:G.78, H:I.103, H:S.104, H:R.113 Water bridges: H:N.13, J:D.89 Salt bridges: H:H.102 FA1.14: 11 residues within 4Å: Chain H: D.89 Chain I: Y.25, N.76, G.78, G.79, H.82, H.102, I.103, S.104, V.106, R.113 10 PLIP interactions: 10 interactions with chain I Hydrophobic interactions: I:Y.25, I:V.106 Hydrogen bonds: I:N.76, I:N.76, I:G.78, I:H.82, I:I.103, I:S.104, I:R.113 Water bridges: I:N.13 FA1.15: 12 residues within 4Å: Chain I: V.85, D.89 Chain J: Y.25, N.76, G.78, G.79, H.82, H.102, I.103, S.104, V.106, R.113 12 PLIP interactions: 12 interactions with chain J Hydrophobic interactions: J:Y.25, J:V.106 Hydrogen bonds: J:N.76, J:N.76, J:G.78, J:H.82, J:H.102, J:I.103, J:S.104, J:R.113 Water bridges: J:G.79 Salt bridges: J:H.102 FA1.16: 12 residues within 4Å: Chain A: V.85, D.89 Chain K: Y.25, N.76, G.78, G.79, H.82, H.102, I.103, S.104, V.106, R.113 12 PLIP interactions: 12 interactions with chain K Hydrophobic interactions: K:Y.25, K:V.106 Hydrogen bonds: K:N.76, K:G.78, K:G.78, K:H.102, K:I.103, K:S.104, K:S.104, K:R.113 Water bridges: K:N.13 Salt bridges: K:H.102 FA1.18: 11 residues within 4Å: Chain K: D.89 Chain L: Y.25, N.76, G.78, G.79, H.82, H.102, I.103, S.104, V.106, R.113 10 PLIP interactions: 10 interactions with chain L Hydrophobic interactions: L:Y.25, L:V.106 Hydrogen bonds: L:N.76, L:G.78, L:I.103, L:S.104, L:S.104, L:R.113 Water bridges: L:N.13 Salt bridges: L:H.102

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain B: N.13, L.14, R.16, L.17, G.18, R.19, R.20, Y.25 Chain E: E.93 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.13, B:G.18, B:R.19, B:R.20, B:R.20 Water bridges: B:P.12, B:N.13 GOL.6: 8 residues within 4Å: Chain C: E.93 Chain E: N.13, R.16, L.17, G.18, R.19, R.20, Y.25 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:N.13, E:G.18, E:R.20 Water bridges: E:N.13 GOL.9: 5 residues within 4Å: Chain G: N.13, R.16, L.17, R.20, Y.25 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:N.13, G:R.20 Water bridges: G:N.13, G:G.18 GOL.11: 5 residues within 4Å: Chain H: N.13, R.16, L.17, R.20, Y.25 7 PLIP interactions: 6 interactions with chain H, 1 interactions with chain J Hydrogen bonds: H:N.13, H:R.20, H:R.20 Water bridges: H:P.12, H:N.13, H:G.18, J:E.93 GOL.13: 6 residues within 4Å: Chain H: E.93 Chain I: N.13, R.16, L.17, R.19, E.21 5 PLIP interactions: 2 interactions with chain H, 3 interactions with chain I Hydrogen bonds: H:E.93, I:N.13, I:R.19 Water bridges: H:D.89, I:G.18 GOL.17: 6 residues within 4Å: Chain K: E.93 Chain L: N.13, R.16, L.17, R.20, Y.25 6 PLIP interactions: 5 interactions with chain L, 1 interactions with chain K Hydrogen bonds: L:N.13, L:R.20, L:R.20 Water bridges: L:N.13, L:G.18, K:D.89

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

2011-05-11

Peptides

3-dehydroquinate dehydratase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

3-dehydroquinate dehydratase

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