SMTL ID : 4zqp.1

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Mycobacterium tuberculosis in the complex with IMP and the inhibitor MAD1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x IMP: INOSINIC ACID(Non-covalent)

IMP.1: 22 residues within 4Å: Chain A: S.86, M.88, N.191, G.216, S.217, I.218, C.219, 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: KP3.2 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:Y.299, A:M.302, A:G.303, A:S.304 Water bridges: A:G.214, A:G.216, A:G.253, A:L.255, A:L.255, A:L.255 IMP.7: 22 residues within 4Å: Chain B: S.86, M.88, N.191, G.216, S.217, I.218, C.219, 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: KP3.8 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:Y.299, B:M.302, B:G.303, B:S.304 Water bridges: B:G.214, B:G.216, B:G.253, B:L.255, B:L.255, B:L.255 IMP.13: 22 residues within 4Å: Chain C: S.86, M.88, N.191, G.216, S.217, I.218, C.219, 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: KP3.14 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:Y.299, C:M.302, C:G.303, C:S.304 Water bridges: C:G.214, C:G.216, C:G.253, C:L.255, C:L.255, C:L.255 IMP.19: 22 residues within 4Å: Chain D: S.86, M.88, N.191, G.216, S.217, I.218, C.219, 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: KP3.20 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:Y.299, D:M.302, D:G.303, D:S.304 Water bridges: D:G.214, D:G.216, D:G.253, D:L.255, D:L.255, D:L.255

4 x KP3: 5'-O-({1-[(2E)-4-(4-hydroxy-6-methoxy-7-methyl-3-oxo-1,3-dihydro-2-benzofuran-5-yl)-2-methylbut-2-en-1-yl]-1H-1,2,3-triazol-4-yl}methyl)adenosine(Non-covalent)

KP3.2: 23 residues within 4Å: Chain A: R.111, D.161, T.162, A.163, H.164, N.167, L.169, V.170, N.191, G.212, V.213, G.214, C.219, T.221, M.302, G.303, E.336 Chain C: V.62, P.64, A.361, G.364, Y.365 Ligands: IMP.1 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:A.163 Hydrogen bonds: A:A.163, A:N.167, A:G.214, A:T.221, A:T.221, C:A.361, C:Y.365 Water bridges: A:R.111 pi-Stacking: A:H.164 KP3.8: 23 residues within 4Å: Chain B: R.111, D.161, T.162, A.163, H.164, N.167, L.169, V.170, N.191, G.212, V.213, G.214, C.219, T.221, M.302, G.303, E.336 Chain D: V.62, P.64, A.361, G.364, Y.365 Ligands: IMP.7 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:A.163 Hydrogen bonds: B:A.163, B:N.167, B:G.214, B:T.221, B:T.221, D:A.361, D:Y.365 Water bridges: B:R.111 pi-Stacking: B:H.164 KP3.14: 23 residues within 4Å: Chain B: V.62, P.64, A.361, G.364, Y.365 Chain C: R.111, D.161, T.162, A.163, H.164, N.167, L.169, V.170, N.191, G.212, V.213, G.214, C.219, T.221, M.302, G.303, E.336 Ligands: IMP.13 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain C Hydrogen bonds: B:A.361, B:Y.365, C:A.163, C:N.167, C:G.214, C:T.221, C:T.221 Hydrophobic interactions: C:A.163 Water bridges: C:R.111 pi-Stacking: C:H.164 KP3.20: 23 residues within 4Å: Chain A: V.62, P.64, A.361, G.364, Y.365 Chain D: R.111, D.161, T.162, A.163, H.164, N.167, L.169, V.170, N.191, G.212, V.213, G.214, C.219, T.221, M.302, G.303, E.336 Ligands: IMP.19 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:A.163 Hydrogen bonds: D:A.163, D:N.167, D:G.214, D:T.221, D:T.221, A:A.361, A:Y.365 Water bridges: D:R.111 pi-Stacking: D:H.164

4 x K: POTASSIUM ION(Non-covalent)

K.3: 7 residues within 4Å: Chain A: G.214, P.215, G.216, C.219 Chain C: E.389, S.390, H.391 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Metal complexes: A:G.214, A:G.216, A:C.219, C:E.389, C:S.390 K.9: 7 residues within 4Å: Chain B: G.214, P.215, G.216, C.219 Chain D: E.389, S.390, H.391 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Metal complexes: B:G.214, B:G.216, B:C.219, D:E.389, D:S.390 K.15: 7 residues within 4Å: Chain B: E.389, S.390, H.391 Chain C: G.214, P.215, G.216, C.219 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Metal complexes: B:E.389, B:S.390, C:G.214, C:G.216, C:C.219 K.21: 7 residues within 4Å: Chain A: E.389, S.390, H.391 Chain D: G.214, P.215, G.216, C.219 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Metal complexes: A:E.389, A:S.390, D:G.214, D:G.216, D:C.219

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 4 residues within 4Å: Chain A: L.277, Q.354, P.402, Y.405 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.405 Water bridges: A:N.403 PO4.10: 4 residues within 4Å: Chain B: L.277, Q.354, P.402, Y.405 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.405 Water bridges: B:N.403 PO4.16: 4 residues within 4Å: Chain C: L.277, Q.354, P.402, Y.405 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.405 Water bridges: C:N.403 PO4.22: 4 residues within 4Å: Chain D: L.277, Q.354, P.402, Y.405 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.405 Water bridges: D:N.403

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: D.51, Q.256, Y.257, D.260 Chain C: K.388, H.393, D.394 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:K.388, C:K.388, C:H.393, C:D.394, A:D.260 Water bridges: A:D.51 GOL.11: 7 residues within 4Å: Chain B: D.51, Q.256, Y.257, D.260 Chain D: K.388, H.393, D.394 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:K.388, D:K.388, D:H.393, D:D.394, B:D.260 Water bridges: B:D.51 GOL.17: 7 residues within 4Å: Chain B: K.388, H.393, D.394 Chain C: D.51, Q.256, Y.257, D.260 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:K.388, B:K.388, B:H.393, B:D.394, C:D.260 Water bridges: C:D.51 GOL.23: 7 residues within 4Å: Chain A: K.388, H.393, D.394 Chain D: D.51, Q.256, Y.257, D.260 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:K.388, A:K.388, A:H.393, A:D.394, D:D.260 Water bridges: D:D.51

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

PGO.6: 9 residues within 4Å: Chain A: D.51, D.52, I.382, T.383, P.384, L.387 Chain C: T.383, P.384, A.385 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:L.387, C:A.385 Hydrogen bonds: A:D.52, A:I.382, C:T.383, C:A.385 PGO.12: 9 residues within 4Å: Chain B: D.51, D.52, I.382, T.383, P.384, L.387 Chain D: T.383, P.384, A.385 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:A.385, B:L.387 Hydrogen bonds: D:T.383, D:A.385, B:D.52, B:I.382 PGO.18: 9 residues within 4Å: Chain B: T.383, P.384, A.385 Chain C: D.51, D.52, I.382, T.383, P.384, L.387 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.387, B:A.385 Hydrogen bonds: C:D.52, C:I.382, B:T.383, B:A.385 PGO.24: 9 residues within 4Å: Chain A: T.383, P.384, A.385 Chain D: D.51, D.52, I.382, T.383, P.384, L.387 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:L.387, A:A.385 Hydrogen bonds: D:D.52, D:I.382, A:T.383, A:A.385

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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