SMTL ID : 1mew.1

Inosine Monophosphate Dehydrogenase (IMPDH) From Tritrichomonas Foetus with XMP and NAD bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 6 residues within 4Å: Chain A: D.264, F.266 Chain C: P.19, G.20, S.22, N.460 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Metal complexes: C:G.20, C:S.22, C:N.460, A:D.264, A:F.266 K.4: 6 residues within 4Å: Chain B: D.264, F.266 Chain D: P.19, G.20, S.22, N.460 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Metal complexes: D:G.20, D:S.22, D:N.460, B:D.264, B:F.266 K.7: 6 residues within 4Å: Chain B: P.19, G.20, S.22, N.460 Chain C: D.264, F.266 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Metal complexes: C:D.264, C:F.266, B:G.20, B:S.22, B:N.460 K.10: 6 residues within 4Å: Chain A: P.19, G.20, S.22, N.460 Chain D: D.264, F.266 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Metal complexes: D:D.264, D:F.266, A:G.20, A:S.22, A:N.460

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

XMP.2: 20 residues within 4Å: Chain A: A.57, M.59, N.291, G.316, S.317, D.358, G.359, G.360, M.379, L.380, G.381, R.382, Y.405, G.407, E.408, G.409, S.410, E.431, G.432 Ligands: NAD.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:N.291, A:S.317, A:G.360, A:G.381, A:R.382, A:Y.405, A:Y.405, A:E.408, A:G.409, A:S.410, A:E.431 Water bridges: A:K.310, A:D.358, A:D.358, A:G.359, A:I.361, A:Y.383 XMP.5: 20 residues within 4Å: Chain B: A.57, M.59, N.291, G.316, S.317, D.358, G.359, G.360, M.379, L.380, G.381, R.382, Y.405, G.407, E.408, G.409, S.410, E.431, G.432 Ligands: NAD.6 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:N.291, B:S.317, B:G.360, B:G.381, B:R.382, B:Y.405, B:Y.405, B:E.408, B:G.409, B:S.410, B:E.431 Water bridges: B:K.310, B:D.358, B:D.358, B:G.359, B:I.361, B:Y.383 XMP.8: 20 residues within 4Å: Chain C: A.57, M.59, N.291, G.316, S.317, D.358, G.359, G.360, M.379, L.380, G.381, R.382, Y.405, G.407, E.408, G.409, S.410, E.431, G.432 Ligands: NAD.9 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:N.291, C:S.317, C:G.360, C:G.381, C:R.382, C:Y.405, C:Y.405, C:E.408, C:G.409, C:S.410, C:E.431 Water bridges: C:K.310, C:D.358, C:D.358, C:G.359, C:I.361, C:Y.383 XMP.11: 20 residues within 4Å: Chain D: A.57, M.59, N.291, G.316, S.317, D.358, G.359, G.360, M.379, L.380, G.381, R.382, Y.405, G.407, E.408, G.409, S.410, E.431, G.432 Ligands: NAD.12 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:N.291, D:S.317, D:G.360, D:G.381, D:R.382, D:Y.405, D:Y.405, D:E.408, D:G.409, D:S.410, D:E.431 Water bridges: D:K.310, D:D.358, D:D.358, D:G.359, D:I.361, D:Y.383

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

NAD.3: 13 residues within 4Å: Chain A: T.240, R.241, D.261, S.262, S.263, W.269, G.312, I.313, G.314, E.408, G.409, E.431 Ligands: XMP.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:E.431 Hydrogen bonds: A:T.240, A:R.241, A:R.241, A:D.261, A:D.261, A:S.263, A:G.312, A:G.314 Water bridges: A:D.261, A:S.262, A:S.262, A:S.262, A:D.264, A:N.291, A:K.310, A:D.358 pi-Stacking: A:W.269, A:W.269 pi-Cation interactions: A:R.241, A:R.241 NAD.6: 13 residues within 4Å: Chain B: T.240, R.241, D.261, S.262, S.263, W.269, G.312, I.313, G.314, E.408, G.409, E.431 Ligands: XMP.5 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:E.431 Hydrogen bonds: B:T.240, B:R.241, B:R.241, B:D.261, B:D.261, B:S.263, B:G.312, B:G.314 Water bridges: B:D.261, B:S.262, B:S.262, B:S.262, B:D.264, B:N.291, B:K.310, B:D.358 pi-Stacking: B:W.269, B:W.269 pi-Cation interactions: B:R.241, B:R.241 NAD.9: 13 residues within 4Å: Chain C: T.240, R.241, D.261, S.262, S.263, W.269, G.312, I.313, G.314, E.408, G.409, E.431 Ligands: XMP.8 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:E.431 Hydrogen bonds: C:T.240, C:R.241, C:R.241, C:D.261, C:D.261, C:S.263, C:G.312, C:G.314 Water bridges: C:D.261, C:S.262, C:S.262, C:S.262, C:D.264, C:N.291, C:K.310, C:D.358 pi-Stacking: C:W.269, C:W.269 pi-Cation interactions: C:R.241, C:R.241 NAD.12: 13 residues within 4Å: Chain D: T.240, R.241, D.261, S.262, S.263, W.269, G.312, I.313, G.314, E.408, G.409, E.431 Ligands: XMP.11 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:E.431 Hydrogen bonds: D:T.240, D:R.241, D:R.241, D:D.261, D:D.261, D:S.263, D:G.312, D:G.314 Water bridges: D:D.261, D:S.262, D:S.262, D:S.262, D:D.264, D:N.291, D:K.310, D:D.358 pi-Stacking: D:W.269, D:W.269 pi-Cation interactions: D:R.241, D:R.241

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prosise, G.L. et al., Crystal Structures of Tritrichomonas foetus Inosine Monophosphate Dehydrogenase in Complex with Substrate, Cofactor and Analogs: A Structural Basis for the Random-in Ordered-out Kinetic Mechanism. J.Mol.Biol. (2003)

Release Date

2003-08-12

Peptides

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

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