SMTL ID : 9i0m.1

Mycobacterium smegmatis inosine monophosphate dehydrogenase (IMPDH) saturating ATP+IMP-bound form, extended

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

8 x IMP: INOSINIC ACID

IMP.1: 18 residues within 4Å: Chain A: S.67, M.69, G.322, S.323, I.324, C.325, D.358, G.359, G.360, G.381, S.382, Y.405, G.407, M.408, G.409, S.410, E.442, G.443 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.67, A:S.67, A:S.323, A:S.323, A:G.360, A:L.361, A:G.381, A:S.382, A:Y.405, A:M.408, A:G.409, A:S.410, A:E.442 IMP.3: 17 residues within 4Å: Chain B: S.67, M.69, G.322, S.323, I.324, C.325, D.358, G.359, G.360, G.381, S.382, Y.405, G.407, M.408, G.409, E.442, G.443 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.67, B:S.323, B:G.360, B:G.381, B:S.382, B:Y.405, B:M.408, B:G.409, B:S.410, B:E.442 IMP.5: 18 residues within 4Å: Chain C: S.67, M.69, G.322, S.323, I.324, C.325, D.358, G.359, G.360, G.381, S.382, Y.405, G.407, M.408, G.409, S.410, E.442, G.443 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:S.67, C:S.323, C:S.323, C:G.360, C:L.361, C:G.381, C:S.382, C:Y.405, C:M.408, C:G.409, C:S.410, C:E.442 IMP.7: 17 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, G.381, S.382, Y.405, G.407, M.408, G.409, E.442 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:S.67, D:S.67, D:N.297, D:S.323, D:S.323, D:D.358, D:G.360, D:G.381, D:S.382, D:Y.405, D:M.408, D:G.409, D:S.410, D:E.442 IMP.9: 18 residues within 4Å: Chain E: S.67, M.69, G.322, S.323, I.324, C.325, D.358, G.359, G.360, G.381, S.382, Y.405, G.407, M.408, G.409, S.410, E.442, G.443 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:S.67, E:S.67, E:S.323, E:S.323, E:G.360, E:G.381, E:S.382, E:M.408, E:G.409, E:S.410, E:E.442 IMP.11: 18 residues within 4Å: Chain F: S.67, M.69, G.322, S.323, I.324, C.325, D.358, G.359, G.360, G.381, S.382, Y.405, G.407, M.408, G.409, S.410, E.442, G.443 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:S.67, F:D.358, F:G.360, F:G.381, F:S.382, F:Y.405, F:M.408, F:G.409, F:S.410, F:E.442 IMP.13: 18 residues within 4Å: Chain G: S.67, M.69, G.322, S.323, I.324, C.325, D.358, G.359, G.360, G.381, S.382, Y.405, G.407, M.408, G.409, S.410, E.442, G.443 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:S.67, G:S.67, G:S.323, G:D.358, G:G.360, G:G.381, G:S.382, G:Y.405, G:M.408, G:G.409, G:S.410, G:E.442 IMP.16: 18 residues within 4Å: Chain H: S.67, M.69, G.322, S.323, I.324, C.325, D.358, G.359, G.360, G.381, S.382, Y.405, G.407, M.408, G.409, S.410, E.442, G.443 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:S.67, H:S.323, H:S.323, H:D.358, H:G.360, H:G.381, H:S.382, H:M.408, H:G.409, H:E.442

8 x K: POTASSIUM ION

K.2: 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 A, 1 interactions with chain B Metal complexes: A:G.322, A:C.325, B:S.496 K.4: 7 residues within 4Å: Chain B: G.320, P.321, G.322, C.325 Chain D: E.495, S.496, H.497 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Metal complexes: B:G.320, B:G.322, D:S.496 K.6: 6 residues within 4Å: Chain A: E.495, S.496, H.497 Chain C: G.320, G.322, C.325 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Metal complexes: C:G.322, C:C.325, A:S.496 K.8: 5 residues within 4Å: Chain C: E.495, S.496 Chain D: G.320, G.322, C.325 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:G.320, D:G.322, D:C.325 K.10: 6 residues within 4Å: Chain E: G.320, 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.12: 7 residues within 4Å: Chain E: E.495, S.496, H.497, H.499 Chain F: G.320, G.322, C.325 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E Metal complexes: F:G.320, F:G.322, F:C.325, E:E.495, E:S.496 K.14: 6 residues within 4Å: Chain F: E.495, S.496, H.497 Chain G: G.320, G.322, C.325 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain F Metal complexes: G:G.320, G:G.322, G:C.325, F:S.496 K.15: 7 residues within 4Å: Chain G: E.495, S.496, H.497, P.498 Chain H: G.320, G.322, C.325 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain H Metal complexes: 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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