SMTL ID : 9i0k.1

Mycobacterium smegmatis inosine monophosphate dehydrogenase (IMPDH) E-XMP* intermediate, compressed

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

8 x IMP: INOSINIC ACID

IMP.1: 21 residues within 4Å: Chain A: S.67, M.69, N.297, G.322, S.323, I.324, C.325, D.358, G.359, G.360, M.379, G.381, S.382, Y.405, G.407, M.408, G.409, S.410, E.442, G.443 Ligands: NAD.2 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:S.67, A:N.297, A:S.323, A:D.358, A:G.360, A:G.381, A:S.382, A:S.382, A:Y.405, A:M.408, A:G.409, A:S.410, A:E.442 Water bridges: A:A.68, A:K.316, A:G.322, A:G.359, A:L.361, A:L.383 IMP.5: 21 residues within 4Å: Chain B: S.67, M.69, N.297, G.322, S.323, I.324, C.325, D.358, G.359, G.360, M.379, G.381, S.382, Y.405, G.407, M.408, G.409, S.410, E.442, G.443 Ligands: NAD.6 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:S.67, B:N.297, B:S.323, B:D.358, B:G.360, B:G.381, B:S.382, B:Y.405, B:M.408, B:G.409, B:S.410, B:E.442 Water bridges: B:K.316, B:K.316, B:G.322, B:G.359, B:L.361, B:L.383 IMP.8: 20 residues within 4Å: Chain C: S.67, N.297, G.322, S.323, I.324, C.325, D.358, G.359, G.360, M.379, G.381, S.382, Y.405, G.407, M.408, G.409, S.410, E.442, G.443 Ligands: NAD.9 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:S.67, C:N.297, C:D.358, C:G.360, C:G.381, C:S.382, C:Y.405, C:M.408, C:G.409, C:E.442 Water bridges: C:A.68, C:K.316, C:G.320, C:G.322, C:G.359, C:G.359, C:L.361, C:S.382 IMP.11: 20 residues within 4Å: Chain D: S.67, M.69, N.297, G.322, S.323, I.324, C.325, D.358, G.359, G.360, M.379, G.381, S.382, Y.405, G.407, M.408, G.409, E.442, G.443 Ligands: NAD.12 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:S.67, D:N.297, D:D.358, D:G.360, D:G.381, D:S.382, D:Y.405, D:M.408, D:G.409, D:E.442 Water bridges: D:G.322, D:G.359, D:L.361, D:L.361, D:S.382 IMP.13: 19 residues within 4Å: Chain E: S.67, M.69, G.322, S.323, I.324, C.325, D.358, G.359, G.360, M.379, G.381, S.382, Y.405, G.407, M.408, G.409, E.442, G.443 Ligands: NAD.14 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:S.67, E:N.297, E:D.358, E:G.360, E:G.381, E:S.382, E:S.382, E:S.382, E:M.408, E:G.409, E:S.410, E:E.442 Water bridges: E:K.316, E:K.316, E:G.322, E:G.359, E:L.361 IMP.17: 22 residues within 4Å: Chain F: S.67, M.69, N.297, G.322, S.323, I.324, C.325, D.358, G.359, G.360, M.379, L.380, G.381, S.382, Y.405, G.407, M.408, G.409, S.410, E.442, G.443 Ligands: NAD.18 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:S.67, F:N.297, F:K.316, F:G.360, F:G.381, F:S.382, F:M.408, F:G.409, F:E.442 Water bridges: F:G.320, F:G.322, F:G.359, F:L.361, F:L.361, F:S.382 IMP.20: 22 residues within 4Å: Chain G: S.67, M.69, N.297, K.316, G.322, S.323, I.324, C.325, D.358, G.359, G.360, M.379, G.381, S.382, Y.405, G.407, M.408, G.409, S.410, E.442, G.443 Ligands: NAD.21 17 PLIP interactions: 17 interactions with chain G Hydrogen bonds: G:S.67, G:N.297, G:K.316, G:G.360, G:G.381, G:S.382, G:M.408, G:G.409, G:S.410, G:E.442 Water bridges: G:A.68, G:K.316, G:G.322, G:G.359, G:G.359, G:L.361, G:S.382 IMP.23: 22 residues within 4Å: Chain H: S.67, M.69, N.297, K.316, G.322, S.323, I.324, C.325, D.358, G.359, G.360, M.379, G.381, S.382, Y.405, G.407, M.408, G.409, S.410, E.442, G.443 Ligands: NAD.24 18 PLIP interactions: 18 interactions with chain H Hydrogen bonds: H:S.67, H:N.297, H:K.316, H:S.323, H:G.360, H:G.381, H:S.382, H:M.408, H:G.409, H:S.410, H:E.442 Water bridges: H:K.316, H:K.316, H:G.322, H:G.359, H:L.361, H:L.361, H:S.382

8 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

NAD.2: 18 residues within 4Å: Chain A: R.92, D.267, T.268, A.269, H.270, N.273, N.297, G.318, V.319, G.320, C.325, T.327, M.408 Chain B: V.43, A.467, G.470, Y.471 Ligands: IMP.1 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.269 Hydrogen bonds: A:D.267, A:A.269, A:N.273, A:G.318, A:G.320, B:A.467 Water bridges: A:N.297 Salt bridges: A:R.92 pi-Stacking: A:H.270 NAD.6: 20 residues within 4Å: Chain B: R.92, D.267, T.268, A.269, H.270, N.273, V.276, N.297, G.318, V.319, G.320, C.325, T.327, M.408 Chain C: V.43, P.45, A.467, G.470, Y.471 Ligands: IMP.5 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:A.269 Hydrogen bonds: B:D.267, B:T.268, B:A.269, B:N.273, B:G.318, B:G.320, C:A.467 Water bridges: B:N.297 Salt bridges: B:R.92 pi-Stacking: B:H.270 NAD.9: 21 residues within 4Å: Chain C: R.92, D.267, T.268, A.269, H.270, N.273, V.276, N.297, G.318, V.319, G.320, C.325, T.327, M.408, G.409, E.442 Chain D: V.43, A.467, G.470, Y.471 Ligands: IMP.8 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:A.269 Hydrogen bonds: C:D.267, C:A.269, C:N.273, C:G.318, C:G.320, D:A.467 Water bridges: C:N.297 Salt bridges: C:R.92 pi-Stacking: C:H.270 NAD.12: 20 residues within 4Å: Chain A: V.43, P.45, A.467, G.470, Y.471 Chain D: R.92, D.267, T.268, A.269, H.270, N.273, N.297, G.318, V.319, G.320, C.325, T.327, M.408, G.409 Ligands: IMP.11 10 PLIP interactions: 1 interactions with chain A, 9 interactions with chain D Hydrogen bonds: A:A.467, D:D.267, D:A.269, D:N.273, D:G.318, D:G.320 Hydrophobic interactions: D:A.269 Water bridges: D:N.297 Salt bridges: D:R.92 pi-Stacking: D:H.270 NAD.14: 19 residues within 4Å: Chain E: R.92, D.267, T.268, A.269, H.270, N.273, N.297, G.318, V.319, G.320, C.325, T.327, M.408, G.409 Chain H: V.43, A.467, G.470, Y.471 Ligands: IMP.13 11 PLIP interactions: 1 interactions with chain H, 10 interactions with chain E Hydrogen bonds: H:A.467, E:R.92, E:D.267, E:A.269, E:N.273, E:G.318, E:G.320 Hydrophobic interactions: E:A.269 Water bridges: E:N.297 Salt bridges: E:R.92 pi-Stacking: E:H.270 NAD.18: 22 residues within 4Å: Chain E: V.43, P.45, A.467, G.470, Y.471 Chain F: R.92, D.267, T.268, A.269, H.270, N.273, V.276, N.297, G.318, V.319, G.320, C.325, T.327, M.408, G.409, E.442 Ligands: IMP.17 10 PLIP interactions: 9 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:A.269 Hydrogen bonds: F:D.267, F:A.269, F:N.273, F:G.318, F:G.320, E:A.467 Water bridges: F:N.297 Salt bridges: F:R.92 pi-Stacking: F:H.270 NAD.21: 20 residues within 4Å: Chain F: V.43, P.45, A.467, G.470, Y.471 Chain G: R.92, D.267, T.268, A.269, H.270, N.273, N.297, G.318, V.319, G.320, C.325, T.327, M.408, G.409 Ligands: IMP.20 10 PLIP interactions: 9 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: G:A.269 Hydrogen bonds: G:D.267, G:A.269, G:N.273, G:G.318, G:G.320, F:A.467 Water bridges: G:N.297 Salt bridges: G:R.92 pi-Stacking: G:H.270 NAD.24: 20 residues within 4Å: Chain G: V.43, P.45, A.467, G.470, Y.471 Chain H: R.92, D.267, T.268, A.269, H.270, N.273, N.297, G.318, V.319, G.320, C.325, T.327, M.408, G.409 Ligands: IMP.23 10 PLIP interactions: 9 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:A.269 Hydrogen bonds: H:D.267, H:A.269, H:N.273, H:G.318, H:G.320, G:A.467 Water bridges: H:N.297 Salt bridges: H:R.92 pi-Stacking: H:H.270

8 x K: POTASSIUM ION

K.3: 7 residues within 4Å: Chain A: E.495, S.496, H.497 Chain D: G.320, P.321, G.322, C.325 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Metal complexes: A:E.495, A:S.496, D:G.322 K.4: 6 residues within 4Å: Chain A: G.320, G.322, C.325 Chain B: E.495, S.496, H.497 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:E.495, B:S.496, A:G.322 K.7: 6 residues within 4Å: Chain B: G.320, G.322, C.325 Chain C: E.495, S.496, H.497 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Metal complexes: B:G.322, B:C.325, C:E.495, C:S.496 K.10: 6 residues within 4Å: Chain C: G.320, G.322, C.325 Chain D: E.495, S.496, H.497 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Metal complexes: C:G.320, C:G.322, D:E.495, D:S.496 K.15: 7 residues within 4Å: Chain E: G.320, P.321, G.322, C.325 Chain H: E.495, S.496, H.497 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain E Metal complexes: H:E.495, H:S.496, E:G.320, E:G.322 K.16: 7 residues within 4Å: Chain E: E.495, S.496, H.497 Chain F: G.320, P.321, G.322, C.325 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain E Metal complexes: F:G.322, E:E.495, E:S.496 K.19: 7 residues within 4Å: Chain F: E.495, S.496, H.497 Chain G: G.320, P.321, G.322, C.325 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain F Metal complexes: G:G.320, G:G.322, G:C.325, F:E.495, F:S.496 K.22: 6 residues within 4Å: Chain G: E.495, S.496, H.497 Chain H: G.320, G.322, C.325 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain H Metal complexes: G:E.495, G:S.496, H:G.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bulvas, O. et al., Conformational landscape of the mycobacterial inosine 5'-monophosphate dehydrogenase octamerization interface. J.Struct.Biol. (2025)

Release Date

2025-03-26

Peptides

Inosine-5'-monophosphate dehydrogenase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Inosine-5'-monophosphate dehydrogenase

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