SMTL ID : 4zqm.1

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Mycobacterium tuberculosis in the complex with XMP and NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x XMP: XANTHOSINE-5'-MONOPHOSPHATE(Non-covalent)

XMP.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: NAD.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:S.86, A:N.191, A:S.217, A:G.254, A:G.275, A:S.276, A:Y.299, A:Y.299, A:M.302, A:G.303, A:S.304, A:E.336 Water bridges: A:G.212, A:G.214, A:G.216, A:T.221, A:G.253, A:L.255, A:S.276, A:S.276 XMP.3: 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: NAD.4 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:S.86, B:N.191, B:S.217, B:G.254, B:G.275, B:S.276, B:Y.299, B:Y.299, B:M.302, B:G.303, B:S.304, B:E.336 Water bridges: B:G.212, B:G.214, B:G.216, B:T.221, B:G.253, B:L.255, B:S.276, B:S.276 XMP.5: 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: NAD.6 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:S.86, C:N.191, C:S.217, C:G.254, C:G.275, C:S.276, C:Y.299, C:Y.299, C:M.302, C:G.303, C:S.304, C:E.336 Water bridges: C:G.212, C:G.214, C:G.216, C:T.221, C:G.253, C:L.255, C:S.276, C:S.276 XMP.7: 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: NAD.8 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:S.86, D:N.191, D:S.217, D:G.254, D:G.275, D:S.276, D:Y.299, D:Y.299, D:M.302, D:G.303, D:S.304, D:E.336 Water bridges: D:G.212, D:G.214, D:G.216, D:T.221, D:G.253, D:L.255, D:S.276, D:S.276

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 18 residues within 4Å: Chain A: R.111, D.161, T.162, A.163, H.164, N.167, L.169, V.170, T.221, M.302, G.303, E.336 Chain C: V.62, P.64, A.361, G.364, Y.365 Ligands: XMP.1 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:A.163 Hydrogen bonds: A:R.111, A:D.161, A:T.162, A:A.163, A:N.167, A:E.336, C:A.361 Water bridges: A:R.111, A:T.162 Salt bridges: A:R.111 pi-Stacking: A:H.164 NAD.4: 18 residues within 4Å: Chain B: R.111, D.161, T.162, A.163, H.164, N.167, L.169, V.170, T.221, M.302, G.303, E.336 Chain D: V.62, P.64, A.361, G.364, Y.365 Ligands: XMP.3 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:A.163 Hydrogen bonds: B:R.111, B:D.161, B:T.162, B:A.163, B:N.167, B:E.336, D:A.361 Water bridges: B:R.111, B:T.162 Salt bridges: B:R.111 pi-Stacking: B:H.164 NAD.6: 18 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, T.221, M.302, G.303, E.336 Ligands: XMP.5 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:A.163 Hydrogen bonds: C:R.111, C:D.161, C:T.162, C:A.163, C:N.167, C:E.336, B:A.361 Water bridges: C:R.111, C:T.162 Salt bridges: C:R.111 pi-Stacking: C:H.164 NAD.8: 18 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, T.221, M.302, G.303, E.336 Ligands: XMP.7 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:A.163 Hydrogen bonds: D:R.111, D:D.161, D:T.162, D:A.163, D:N.167, D:E.336, A:A.361 Water bridges: D:R.111, D:T.162 Salt bridges: D:R.111 pi-Stacking: D:H.164

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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