SMTL ID : 6u8e.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

8 x IMP: INOSINIC ACID(Covalent)

IMP.1: 23 residues within 4Å: Chain A: S.73, M.75, N.308, R.327, G.333, S.334, I.335, C.336, D.369, G.370, G.371, M.390, M.391, G.392, S.393, Y.416, G.418, M.419, G.420, S.421, Q.446, G.447 Ligands: NAD.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.308, A:R.327, A:S.334, A:D.369, A:G.370, A:G.371, A:G.392, A:S.393, A:M.419, A:G.420, A:S.421, A:Q.446 IMP.3: 23 residues within 4Å: Chain B: S.73, M.75, N.308, R.327, G.333, S.334, I.335, C.336, D.369, G.370, G.371, M.390, M.391, G.392, S.393, Y.416, G.418, M.419, G.420, S.421, Q.446, G.447 Ligands: NAD.4 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.308, B:R.327, B:S.334, B:D.369, B:G.370, B:G.371, B:G.392, B:S.393, B:M.419, B:G.420, B:S.421, B:Q.446 IMP.5: 23 residues within 4Å: Chain C: S.73, M.75, N.308, R.327, G.333, S.334, I.335, C.336, D.369, G.370, G.371, M.390, M.391, G.392, S.393, Y.416, G.418, M.419, G.420, S.421, Q.446, G.447 Ligands: NAD.6 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:N.308, C:R.327, C:S.334, C:D.369, C:G.370, C:G.371, C:G.392, C:S.393, C:M.419, C:G.420, C:S.421, C:Q.446 IMP.7: 23 residues within 4Å: Chain D: S.73, M.75, N.308, R.327, G.333, S.334, I.335, C.336, D.369, G.370, G.371, M.390, M.391, G.392, S.393, Y.416, G.418, M.419, G.420, S.421, Q.446, G.447 Ligands: NAD.8 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:N.308, D:R.327, D:S.334, D:D.369, D:G.370, D:G.371, D:G.392, D:S.393, D:M.419, D:G.420, D:S.421, D:Q.446 IMP.9: 23 residues within 4Å: Chain E: S.73, M.75, N.308, R.327, G.333, S.334, I.335, C.336, D.369, G.370, G.371, M.390, M.391, G.392, S.393, Y.416, G.418, M.419, G.420, S.421, Q.446, G.447 Ligands: NAD.10 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:N.308, E:R.327, E:S.334, E:D.369, E:D.369, E:G.370, E:G.371, E:G.392, E:S.393, E:S.393, E:Y.416, E:M.419, E:G.420, E:S.421, E:Q.446 IMP.11: 23 residues within 4Å: Chain F: S.73, M.75, N.308, R.327, G.333, S.334, I.335, C.336, D.369, G.370, G.371, M.390, M.391, G.392, S.393, Y.416, G.418, M.419, G.420, S.421, Q.446, G.447 Ligands: NAD.12 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:N.308, F:R.327, F:S.334, F:D.369, F:D.369, F:G.370, F:G.371, F:G.392, F:S.393, F:S.393, F:Y.416, F:M.419, F:G.420, F:S.421, F:Q.446 IMP.13: 23 residues within 4Å: Chain G: S.73, M.75, N.308, R.327, G.333, S.334, I.335, C.336, D.369, G.370, G.371, M.390, M.391, G.392, S.393, Y.416, G.418, M.419, G.420, S.421, Q.446, G.447 Ligands: NAD.14 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:N.308, G:R.327, G:S.334, G:D.369, G:D.369, G:G.370, G:G.371, G:G.392, G:S.393, G:S.393, G:Y.416, G:M.419, G:G.420, G:S.421, G:Q.446 IMP.15: 23 residues within 4Å: Chain H: S.73, M.75, N.308, R.327, G.333, S.334, I.335, C.336, D.369, G.370, G.371, M.390, M.391, G.392, S.393, Y.416, G.418, M.419, G.420, S.421, Q.446, G.447 Ligands: NAD.16 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:N.308, H:R.327, H:S.334, H:D.369, H:D.369, H:G.370, H:G.371, H:G.392, H:S.393, H:S.393, H:Y.416, H:M.419, H:G.420, H:S.421, H:Q.446

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

NAD.2: 17 residues within 4Å: Chain A: H.98, H.258, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, C.336, T.338, M.419, G.420, Q.446 Chain D: Q.474 Ligands: IMP.1 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:T.338 Hydrogen bonds: A:D.279, A:S.281, A:S.281, A:N.308, A:G.329, A:G.331, D:Q.474 Salt bridges: A:H.258 pi-Stacking: A:F.287, A:F.287 pi-Cation interactions: A:H.258, A:H.258 NAD.4: 17 residues within 4Å: Chain A: Q.474 Chain B: H.98, H.258, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, C.336, T.338, M.419, G.420, Q.446 Ligands: IMP.3 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.338 Hydrogen bonds: B:D.279, B:S.281, B:S.281, B:N.308, B:G.329, B:G.331, A:Q.474 Salt bridges: B:H.258 pi-Stacking: B:F.287, B:F.287 pi-Cation interactions: B:H.258, B:H.258 NAD.6: 18 residues within 4Å: Chain B: T.50, Q.474 Chain C: H.98, H.258, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, C.336, T.338, M.419, G.420, Q.446 Ligands: IMP.5 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:T.338 Hydrogen bonds: C:D.279, C:S.281, C:S.281, C:N.308, C:G.329, C:G.331, B:Q.474 Salt bridges: C:H.258 pi-Stacking: C:F.287, C:F.287 pi-Cation interactions: C:H.258, C:H.258 NAD.8: 17 residues within 4Å: Chain C: Q.474 Chain D: H.98, H.258, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, C.336, T.338, M.419, G.420, Q.446 Ligands: IMP.7 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:T.338 Hydrogen bonds: D:D.279, D:S.281, D:S.281, D:N.308, D:G.329, D:G.331, C:Q.474 Salt bridges: D:H.258 pi-Stacking: D:F.287, D:F.287 pi-Cation interactions: D:H.258, D:H.258 NAD.10: 17 residues within 4Å: Chain E: H.98, H.258, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, C.336, T.338, M.419, G.420, Q.446 Chain H: Q.474 Ligands: IMP.9 13 PLIP interactions: 12 interactions with chain E, 1 interactions with chain H Hydrophobic interactions: E:T.338 Hydrogen bonds: E:D.279, E:S.281, E:S.281, E:N.308, E:G.329, E:G.331, H:Q.474 Salt bridges: E:H.258 pi-Stacking: E:F.287, E:F.287 pi-Cation interactions: E:H.258, E:H.258 NAD.12: 18 residues within 4Å: Chain E: T.50, Q.474 Chain F: H.98, H.258, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, C.336, T.338, M.419, G.420, Q.446 Ligands: IMP.11 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:T.338 Hydrogen bonds: F:D.279, F:S.281, F:S.281, F:N.308, F:G.329, F:G.331, E:Q.474 Salt bridges: F:H.258 pi-Stacking: F:F.287, F:F.287 pi-Cation interactions: F:H.258, F:H.258 NAD.14: 18 residues within 4Å: Chain F: T.50, Q.474 Chain G: H.98, H.258, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, C.336, T.338, M.419, G.420, Q.446 Ligands: IMP.13 13 PLIP interactions: 12 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: G:T.338 Hydrogen bonds: G:D.279, G:S.281, G:S.281, G:N.308, G:G.329, G:G.331, F:Q.474 Salt bridges: G:H.258 pi-Stacking: G:F.287, G:F.287 pi-Cation interactions: G:H.258, G:H.258 NAD.16: 18 residues within 4Å: Chain G: T.50, Q.474 Chain H: H.98, H.258, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, C.336, T.338, M.419, G.420, Q.446 Ligands: IMP.15 13 PLIP interactions: 12 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:T.338 Hydrogen bonds: H:D.279, H:S.281, H:S.281, H:N.308, H:G.329, H:G.331, G:Q.474 Salt bridges: H:H.258 pi-Stacking: H:F.287, H:F.287 pi-Cation interactions: H:H.258, H:H.258

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