SMTL ID : 6u8s.1

Human IMPDH2 treated with ATP, IMP, NAD+, and 2 mM GTP. Filament assembly interface reconstruction.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

8 x IMP: INOSINIC ACID(Covalent)

IMP.1: 20 residues within 4Å: Chain A: S.68, M.70, R.322, G.328, S.329, C.331, D.364, G.365, G.366, M.385, G.387, S.388, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.68, A:R.322, A:S.329, A:S.329, A:D.364, A:G.365, A:G.366, A:G.387, A:S.388, A:S.388, A:M.414, A:G.415, A:S.416, A:Q.441 IMP.3: 20 residues within 4Å: Chain B: S.68, M.70, R.322, G.328, S.329, C.331, D.364, G.365, G.366, M.385, G.387, S.388, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.4 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.68, B:R.322, B:S.329, B:S.329, B:D.364, B:G.365, B:G.366, B:G.387, B:S.388, B:S.388, B:M.414, B:G.415, B:S.416, B:Q.441 IMP.5: 20 residues within 4Å: Chain C: S.68, M.70, R.322, G.328, S.329, C.331, D.364, G.365, G.366, M.385, G.387, S.388, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.6 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:S.68, C:R.322, C:S.329, C:S.329, C:D.364, C:G.365, C:G.366, C:G.387, C:S.388, C:S.388, C:M.414, C:G.415, C:S.416, C:Q.441 IMP.7: 20 residues within 4Å: Chain D: S.68, M.70, R.322, G.328, S.329, C.331, D.364, G.365, G.366, M.385, G.387, S.388, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.8 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:S.68, D:R.322, D:S.329, D:S.329, D:D.364, D:G.365, D:G.366, D:G.387, D:S.388, D:S.388, D:M.414, D:G.415, D:S.416, D:Q.441 IMP.9: 20 residues within 4Å: Chain E: S.68, M.70, R.322, G.328, S.329, C.331, D.364, G.365, G.366, M.385, G.387, S.388, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.10 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:S.68, E:R.322, E:S.329, E:D.364, E:D.364, E:G.365, E:G.366, E:G.387, E:S.388, E:S.388, E:S.388, E:Y.411, E:M.414, E:G.415, E:S.416, E:Q.441 IMP.11: 20 residues within 4Å: Chain F: S.68, M.70, R.322, G.328, S.329, C.331, D.364, G.365, G.366, M.385, G.387, S.388, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.12 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:S.68, F:R.322, F:S.329, F:D.364, F:D.364, F:G.365, F:G.366, F:G.387, F:S.388, F:S.388, F:S.388, F:Y.411, F:M.414, F:G.415, F:S.416, F:Q.441 IMP.13: 20 residues within 4Å: Chain G: S.68, M.70, R.322, G.328, S.329, C.331, D.364, G.365, G.366, M.385, G.387, S.388, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.14 16 PLIP interactions: 16 interactions with chain G Hydrogen bonds: G:S.68, G:R.322, G:S.329, G:D.364, G:D.364, G:G.365, G:G.366, G:G.387, G:S.388, G:S.388, G:S.388, G:Y.411, G:M.414, G:G.415, G:S.416, G:Q.441 IMP.15: 20 residues within 4Å: Chain H: S.68, M.70, R.322, G.328, S.329, C.331, D.364, G.365, G.366, M.385, G.387, S.388, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.16 16 PLIP interactions: 16 interactions with chain H Hydrogen bonds: H:S.68, H:R.322, H:S.329, H:D.364, H:D.364, H:G.365, H:G.366, H:G.387, H:S.388, H:S.388, H:S.388, H:Y.411, H:M.414, H:G.415, H:S.416, H:Q.441

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

NAD.2: 17 residues within 4Å: Chain A: H.93, T.252, H.253, E.254, D.274, S.275, S.276, F.282, N.303, G.324, M.325, G.326, C.331, M.414, Q.441 Chain D: Q.469 Ligands: IMP.1 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:H.93, A:E.254, A:D.274, A:S.276, A:S.276, A:G.324, A:G.326, D:Q.469 Salt bridges: A:H.253 pi-Stacking: A:H.253, A:F.282, A:F.282 NAD.4: 17 residues within 4Å: Chain A: Q.469 Chain B: H.93, T.252, H.253, E.254, D.274, S.275, S.276, F.282, N.303, G.324, M.325, G.326, C.331, M.414, Q.441 Ligands: IMP.3 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.93, B:E.254, B:D.274, B:S.276, B:S.276, B:G.324, B:G.326, A:Q.469 Salt bridges: B:H.253 pi-Stacking: B:H.253, B:F.282, B:F.282 NAD.6: 17 residues within 4Å: Chain B: Q.469 Chain C: H.93, T.252, H.253, E.254, D.274, S.275, S.276, F.282, N.303, G.324, M.325, G.326, C.331, M.414, Q.441 Ligands: IMP.5 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:H.93, C:E.254, C:D.274, C:S.276, C:S.276, C:G.324, C:G.326, B:Q.469 Salt bridges: C:H.253 pi-Stacking: C:H.253, C:F.282, C:F.282 NAD.8: 18 residues within 4Å: Chain C: T.45, Q.469 Chain D: H.93, T.252, H.253, E.254, D.274, S.275, S.276, F.282, N.303, G.324, M.325, G.326, C.331, M.414, Q.441 Ligands: IMP.7 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:H.93, D:E.254, D:D.274, D:S.276, D:S.276, D:G.324, D:G.326, C:Q.469 Salt bridges: D:H.253 pi-Stacking: D:H.253, D:F.282, D:F.282 NAD.10: 17 residues within 4Å: Chain E: H.93, T.252, H.253, E.254, D.274, S.275, S.276, F.282, N.303, G.324, M.325, G.326, C.331, M.414, Q.441 Chain H: Q.469 Ligands: IMP.9 12 PLIP interactions: 11 interactions with chain E, 1 interactions with chain H Hydrogen bonds: E:H.93, E:E.254, E:D.274, E:S.276, E:S.276, E:G.324, E:G.326, H:Q.469 Salt bridges: E:H.253 pi-Stacking: E:H.253, E:F.282, E:F.282 NAD.12: 18 residues within 4Å: Chain E: T.45, Q.469 Chain F: H.93, T.252, H.253, E.254, D.274, S.275, S.276, F.282, N.303, G.324, M.325, G.326, C.331, M.414, Q.441 Ligands: IMP.11 12 PLIP interactions: 11 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:H.93, F:E.254, F:D.274, F:S.276, F:S.276, F:G.324, F:G.326, E:Q.469 Salt bridges: F:H.253 pi-Stacking: F:H.253, F:F.282, F:F.282 NAD.14: 18 residues within 4Å: Chain F: T.45, Q.469 Chain G: H.93, T.252, H.253, E.254, D.274, S.275, S.276, F.282, N.303, G.324, M.325, G.326, C.331, M.414, Q.441 Ligands: IMP.13 12 PLIP interactions: 11 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:H.93, G:E.254, G:D.274, G:S.276, G:S.276, G:G.324, G:G.326, F:Q.469 Salt bridges: G:H.253 pi-Stacking: G:H.253, G:F.282, G:F.282 NAD.16: 17 residues within 4Å: Chain G: Q.469 Chain H: H.93, T.252, H.253, E.254, D.274, S.275, S.276, F.282, N.303, G.324, M.325, G.326, C.331, M.414, Q.441 Ligands: IMP.15 12 PLIP interactions: 11 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:H.93, H:E.254, H:D.274, H:S.276, H:S.276, H:G.324, H:G.326, G:Q.469 Salt bridges: H:H.253 pi-Stacking: H:H.253, H:F.282, H:F.282

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnson, M.C. et al., Cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation. Elife (2020)

Release Date

2020-03-25

Peptides

Inosine-5'-monophosphate dehydrogenase 2: 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 2

Related Entries With Identical Sequence