SMTL ID : 3n86.2 (1 other biounit)

Crystal structure of 3-dehydroquinate dehydratase from Mycobacterium tuberculosis in complex with inhibitor 4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-12-mer

Ligands

12 x RJP: (1R,5R)-1,5-dihydroxy-4-oxo-3-[3-oxo-3-(phenylamino)propyl]cyclohex-2-ene-1-carboxylic acid(Non-covalent)

RJP.1: 19 residues within 4Å: Chain A: P.12, N.13, L.14, R.16, R.20, E.21, Y.25, N.76, G.78, G.79, H.82, H.102, I.103, S.104, V.106, R.113 Chain L: V.85, D.89, E.93 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:N.13, A:L.14, A:R.16, A:R.20, A:E.21, A:Y.25, A:Y.25, A:Y.25, A:V.106 Hydrogen bonds: A:N.13, A:N.76, A:N.76, A:G.78, A:H.102, A:I.103, A:S.104, A:R.113 Water bridges: A:G.79 Salt bridges: A:H.102 RJP.2: 18 residues within 4Å: Chain B: P.12, N.13, L.14, R.16, R.20, E.21, Y.25, N.76, G.78, G.79, H.82, H.102, I.103, S.104, V.106, R.113 Chain E: D.89, E.93 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:N.13, B:L.14, B:R.16, B:E.21, B:E.21, B:Y.25, B:Y.25, B:Y.25, B:V.106 Hydrogen bonds: B:N.13, B:N.76, B:N.76, B:G.78, B:G.78, B:H.102, B:I.103, B:S.104, B:R.113 Water bridges: B:G.79 Salt bridges: B:H.102 RJP.3: 19 residues within 4Å: Chain B: V.85, D.89, E.93 Chain C: P.12, N.13, L.14, R.16, R.20, E.21, Y.25, N.76, G.78, G.79, H.82, H.102, I.103, S.104, V.106, R.113 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:N.13, C:L.14, C:R.16, C:R.20, C:E.21, C:Y.25, C:Y.25, C:V.106 Hydrogen bonds: C:N.13, C:N.76, C:N.76, C:G.78, C:G.78, C:I.103, C:S.104, C:R.113, B:D.89 Salt bridges: C:H.102 RJP.4: 17 residues within 4Å: Chain D: P.12, N.13, R.16, R.20, E.21, Y.25, N.76, G.78, G.79, H.82, H.102, I.103, S.104, V.106, R.113 Chain G: D.89, E.93 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:N.13, D:R.16, D:R.20, D:E.21, D:Y.25, D:Y.25, D:V.106 Hydrogen bonds: D:N.13, D:N.76, D:N.76, D:G.78, D:I.103, D:S.104, D:R.113 Salt bridges: D:H.102 RJP.5: 19 residues within 4Å: Chain C: V.85, D.89, E.93 Chain E: P.12, N.13, L.14, R.16, R.20, E.21, Y.25, N.76, G.78, G.79, H.82, H.102, I.103, S.104, V.106, R.113 18 PLIP interactions: 17 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:N.13, E:L.14, E:R.16, E:R.20, E:E.21, E:Y.25, E:Y.25, E:V.106, C:E.93 Hydrogen bonds: E:N.13, E:N.76, E:N.76, E:G.78, E:H.102, E:I.103, E:S.104, E:R.113 Salt bridges: E:H.102 RJP.6: 18 residues within 4Å: Chain D: D.89, E.93 Chain F: P.12, N.13, L.14, R.16, R.20, E.21, Y.25, N.76, G.78, G.79, H.82, H.102, I.103, S.104, V.106, R.113 18 PLIP interactions: 18 interactions with chain F Hydrophobic interactions: F:N.13, F:L.14, F:R.16, F:R.20, F:E.21, F:Y.25, F:Y.25, F:Y.25, F:V.106 Hydrogen bonds: F:N.13, F:N.76, F:N.76, F:G.78, F:I.103, F:S.104, F:R.113 Water bridges: F:G.79 Salt bridges: F:H.102 RJP.7: 20 residues within 4Å: Chain F: V.85, D.89, E.93 Chain G: P.12, N.13, L.14, R.16, R.20, E.21, Y.25, N.76, G.78, G.79, H.82, H.102, I.103, S.104, V.106, R.109, R.113 17 PLIP interactions: 17 interactions with chain G Hydrophobic interactions: G:N.13, G:L.14, G:R.16, G:R.20, G:E.21, G:Y.25, G:Y.25, G:Y.25, G:V.106 Hydrogen bonds: G:N.13, G:N.76, G:N.76, G:G.78, G:I.103, G:S.104, G:R.113 Salt bridges: G:H.102 RJP.8: 18 residues within 4Å: Chain H: P.12, N.13, L.14, R.16, R.20, E.21, Y.25, N.76, G.78, G.79, H.82, H.102, I.103, S.104, V.106, R.113 Chain J: D.89, E.93 19 PLIP interactions: 18 interactions with chain H, 1 interactions with chain J Hydrophobic interactions: H:N.13, H:L.14, H:R.16, H:R.20, H:E.21, H:Y.25, H:Y.25, H:Y.25, H:V.106, J:E.93 Hydrogen bonds: H:N.13, H:N.76, H:N.76, H:G.78, H:H.102, H:I.103, H:S.104, H:R.113 Salt bridges: H:H.102 RJP.9: 20 residues within 4Å: Chain H: V.85, D.89, E.93 Chain I: P.12, N.13, L.14, R.16, R.20, E.21, Y.25, N.76, G.78, G.79, H.82, H.102, I.103, S.104, V.106, R.109, R.113 19 PLIP interactions: 19 interactions with chain I Hydrophobic interactions: I:N.13, I:L.14, I:R.16, I:R.20, I:E.21, I:Y.25, I:Y.25, I:V.106 Hydrogen bonds: I:N.13, I:N.76, I:N.76, I:G.78, I:G.78, I:H.102, I:I.103, I:S.104, I:R.113 Water bridges: I:G.79 Salt bridges: I:H.102 RJP.10: 16 residues within 4Å: Chain I: V.85, D.89, E.93 Chain J: P.12, N.13, R.16, Y.25, N.76, G.78, G.79, H.82, H.102, I.103, S.104, V.106, R.113 16 PLIP interactions: 2 interactions with chain I, 14 interactions with chain J Hydrophobic interactions: I:E.93, J:N.13, J:R.16, J:Y.25, J:V.106 Hydrogen bonds: I:D.89, J:N.13, J:N.76, J:N.76, J:G.78, J:G.78, J:I.103, J:S.104, J:R.113 Water bridges: J:G.79 Salt bridges: J:H.102 RJP.11: 20 residues within 4Å: Chain A: V.85, D.89, E.93 Chain K: P.12, N.13, L.14, R.16, R.20, E.21, Y.25, N.76, G.78, G.79, H.82, H.102, I.103, S.104, V.106, R.109, R.113 20 PLIP interactions: 19 interactions with chain K, 1 interactions with chain A Hydrophobic interactions: K:N.13, K:L.14, K:R.16, K:R.20, K:E.21, K:E.21, K:Y.25, K:Y.25, K:Y.25, K:V.106 Hydrogen bonds: K:N.13, K:N.76, K:N.76, K:G.78, K:G.78, K:I.103, K:S.104, K:R.113, A:D.89 Salt bridges: K:H.102 RJP.12: 18 residues within 4Å: Chain K: D.89, E.93 Chain L: P.12, N.13, R.16, R.20, E.21, Y.25, N.76, G.78, G.79, H.82, H.102, I.103, S.104, V.106, R.109, R.113 18 PLIP interactions: 18 interactions with chain L Hydrophobic interactions: L:N.13, L:R.16, L:R.20, L:E.21, L:Y.25, L:Y.25, L:Y.25, L:V.106 Hydrogen bonds: L:N.13, L:N.76, L:N.76, L:G.78, L:G.78, L:H.102, L:I.103, L:S.104, L:R.113 Salt bridges: L:H.102

Links

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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
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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