SMTL ID : 4zqo.1

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Mycobacterium tuberculosis in the complex with IMP and the inhibitor Q67

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-tetramer

Ligands

4 x IMP: INOSINIC ACID(Non-covalent)

IMP.1: 23 residues within 4Å: Chain A: S.86, M.88, N.191, G.216, S.217, I.218, C.219, T.221, D.252, G.253, G.254, M.273, L.274, G.275, S.276, Y.299, G.301, M.302, G.303, S.304, E.336, G.337 Ligands: Q67.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.86, A:N.191, A:D.252, A:G.254, A:G.275, A:S.276, A:M.302, A:G.303, A:E.336 Water bridges: A:K.210, A:G.214, A:G.216, A:G.253, A:L.255, A:L.255, A:L.255 IMP.6: 23 residues within 4Å: Chain B: S.86, M.88, N.191, G.216, S.217, I.218, C.219, T.221, D.252, G.253, G.254, M.273, L.274, G.275, S.276, Y.299, G.301, M.302, G.303, S.304, E.336, G.337 Ligands: Q67.7 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:S.86, B:N.191, B:D.252, B:G.254, B:G.275, B:S.276, B:M.302, B:G.303, B:E.336 Water bridges: B:K.210, B:G.214, B:G.216, B:G.253, B:L.255, B:L.255, B:L.255 IMP.11: 23 residues within 4Å: Chain C: S.86, M.88, N.191, G.216, S.217, I.218, C.219, T.221, D.252, G.253, G.254, M.273, L.274, G.275, S.276, Y.299, G.301, M.302, G.303, S.304, E.336, G.337 Ligands: Q67.12 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:S.86, C:N.191, C:D.252, C:G.254, C:G.275, C:S.276, C:M.302, C:G.303, C:E.336 Water bridges: C:K.210, C:G.214, C:G.216, C:G.253, C:L.255, C:L.255, C:L.255 IMP.16: 23 residues within 4Å: Chain D: S.86, M.88, N.191, G.216, S.217, I.218, C.219, T.221, D.252, G.253, G.254, M.273, L.274, G.275, S.276, Y.299, G.301, M.302, G.303, S.304, E.336, G.337 Ligands: Q67.17 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:S.86, D:N.191, D:D.252, D:G.254, D:G.275, D:S.276, D:M.302, D:G.303, D:E.336 Water bridges: D:K.210, D:G.214, D:G.216, D:G.253, D:L.255, D:L.255, D:L.255

4 x Q67: N~2~-(2,3-dichlorophenyl)-N-[2-(pyridin-4-yl)-1,3-benzoxazol-5-yl]-L-alaninamide(Non-covalent)

Q67.2: 16 residues within 4Å: Chain A: A.163, N.167, T.221, M.302, G.303, L.333, V.334, E.336 Chain D: S.60, V.62, V.63, P.64, A.361, G.364, Y.365 Ligands: IMP.1 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:A.163, A:L.333, D:V.63, D:P.64, D:Y.365 Hydrogen bonds: A:E.336, D:Y.365 Water bridges: A:A.163 Q67.7: 16 residues within 4Å: Chain B: A.163, N.167, T.221, M.302, G.303, L.333, V.334, E.336 Chain C: S.60, V.62, V.63, P.64, A.361, G.364, Y.365 Ligands: IMP.6 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:A.163, B:L.333, C:V.63, C:P.64, C:Y.365 Hydrogen bonds: B:E.336, C:Y.365 Water bridges: B:A.163 Q67.12: 16 residues within 4Å: Chain A: S.60, V.62, V.63, P.64, A.361, G.364, Y.365 Chain C: A.163, N.167, T.221, M.302, G.303, L.333, V.334, E.336 Ligands: IMP.11 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:V.63, A:P.64, A:Y.365, C:A.163, C:L.333 Hydrogen bonds: A:Y.365, C:E.336 Water bridges: C:A.163 Q67.17: 16 residues within 4Å: Chain B: S.60, V.62, V.63, P.64, A.361, G.364, Y.365 Chain D: A.163, N.167, T.221, M.302, G.303, L.333, V.334, E.336 Ligands: IMP.16 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:A.163, D:L.333, B:V.63, B:P.64, B:Y.365 Hydrogen bonds: D:E.336, B:Y.365 Water bridges: D:A.163

4 x K: POTASSIUM ION(Non-covalent)

K.3: 7 residues within 4Å: Chain A: G.214, P.215, G.216, C.219 Chain D: E.389, S.390, H.391 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Metal complexes: D:E.389, D:S.390, A:G.214, A:G.216, A:C.219 K.8: 7 residues within 4Å: Chain B: G.214, P.215, G.216, C.219 Chain C: E.389, S.390, H.391 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Metal complexes: B:G.214, B:G.216, B:C.219, C:E.389, C:S.390 K.13: 7 residues within 4Å: Chain A: E.389, S.390, H.391 Chain C: G.214, P.215, G.216, C.219 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Metal complexes: C:G.214, C:G.216, C:C.219, A:E.389, A:S.390 K.18: 7 residues within 4Å: Chain B: E.389, S.390, H.391 Chain D: G.214, P.215, G.216, C.219 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Metal complexes: B:E.389, B:S.390, D:G.214, D:G.216, D:C.219

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: D.51, Q.256, Y.257, D.260 Chain D: K.388, H.393, D.394 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:K.388, D:K.388, D:D.394, A:D.260 Water bridges: A:D.51 GOL.9: 7 residues within 4Å: Chain B: D.51, Q.256, Y.257, D.260 Chain C: K.388, H.393, D.394 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:D.260, C:K.388, C:K.388, C:D.394 Water bridges: B:D.51 GOL.14: 7 residues within 4Å: Chain A: K.388, H.393, D.394 Chain C: D.51, Q.256, Y.257, D.260 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:K.388, A:K.388, A:D.394, C:D.260 Water bridges: C:D.51 GOL.19: 7 residues within 4Å: Chain B: K.388, H.393, D.394 Chain D: D.51, Q.256, Y.257, D.260 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:K.388, B:K.388, B:D.394, D:D.260 Water bridges: D:D.51

4 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.5: 4 residues within 4Å: Chain A: Q.72, G.246, P.248, S.270 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.270 Water bridges: A:G.246, A:S.270, A:E.372 PGO.10: 4 residues within 4Å: Chain B: Q.72, G.246, P.248, S.270 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.270 Water bridges: B:G.246, B:S.270, B:E.372 PGO.15: 4 residues within 4Å: Chain C: Q.72, G.246, P.248, S.270 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.270 Water bridges: C:G.246, C:S.270, C:E.372 PGO.20: 4 residues within 4Å: Chain D: Q.72, G.246, P.248, S.270 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.270 Water bridges: D:G.246, D:S.270, D:E.372

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Makowska-Grzyska, M. et al., Mycobacterium tuberculosis IMPDH in Complexes with Substrates, Products and Antitubercular Compounds. Plos One (2015)

Release Date

2015-06-17

Peptides

Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase

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