SMTL ID : 8u8y.1

Human retinal variant phosphomimetic IMPDH1(546)-S477D filament bound by ATP, IMP, and NAD+, interface-centered

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

8 x IMP: INOSINIC ACID(Non-covalent)

IMP.1: 23 residues within 4Å: Chain A: S.70, M.72, R.324, G.330, S.331, I.332, C.333, T.335, D.366, G.367, G.368, M.387, M.388, G.389, S.390, Y.413, G.415, M.416, G.417, S.418, Q.443, G.444 Ligands: NAD.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.70, A:S.70, A:R.324, A:S.331, A:D.366, A:G.368, A:G.389, A:S.390, A:M.416, A:G.417, A:S.418, A:Q.443 IMP.3: 23 residues within 4Å: Chain B: S.70, M.72, R.324, G.330, S.331, I.332, C.333, T.335, D.366, G.367, G.368, M.387, M.388, G.389, S.390, Y.413, G.415, M.416, G.417, S.418, Q.443, G.444 Ligands: NAD.4 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.70, B:S.70, B:R.324, B:S.331, B:D.366, B:G.368, B:G.389, B:S.390, B:M.416, B:G.417, B:S.418, B:Q.443 IMP.5: 23 residues within 4Å: Chain C: S.70, M.72, R.324, G.330, S.331, I.332, C.333, T.335, D.366, G.367, G.368, M.387, M.388, G.389, S.390, Y.413, G.415, M.416, G.417, S.418, Q.443, G.444 Ligands: NAD.6 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:S.70, C:S.70, C:R.324, C:S.331, C:D.366, C:G.368, C:G.389, C:S.390, C:M.416, C:G.417, C:S.418, C:Q.443 IMP.7: 23 residues within 4Å: Chain D: S.70, M.72, R.324, G.330, S.331, I.332, C.333, T.335, D.366, G.367, G.368, M.387, M.388, G.389, S.390, Y.413, G.415, M.416, G.417, S.418, Q.443, G.444 Ligands: NAD.8 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:S.70, D:S.70, D:R.324, D:S.331, D:D.366, D:G.368, D:G.389, D:S.390, D:M.416, D:G.417, D:S.418, D:Q.443 IMP.9: 23 residues within 4Å: Chain E: S.70, M.72, R.324, G.330, S.331, I.332, C.333, T.335, D.366, G.367, G.368, M.387, M.388, G.389, S.390, Y.413, G.415, M.416, G.417, S.418, Q.443, G.444 Ligands: NAD.10 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:S.70, E:S.70, E:R.324, E:S.331, E:D.366, E:G.368, E:G.389, E:S.390, E:S.390, E:Y.413, E:M.416, E:G.417, E:S.418, E:Q.443 IMP.11: 23 residues within 4Å: Chain F: S.70, M.72, R.324, G.330, S.331, I.332, C.333, T.335, D.366, G.367, G.368, M.387, M.388, G.389, S.390, Y.413, G.415, M.416, G.417, S.418, Q.443, G.444 Ligands: NAD.12 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:S.70, F:S.70, F:R.324, F:S.331, F:D.366, F:G.368, F:G.389, F:S.390, F:S.390, F:Y.413, F:M.416, F:G.417, F:S.418, F:Q.443 IMP.13: 23 residues within 4Å: Chain G: S.70, M.72, R.324, G.330, S.331, I.332, C.333, T.335, D.366, G.367, G.368, M.387, M.388, G.389, S.390, Y.413, G.415, M.416, G.417, S.418, Q.443, G.444 Ligands: NAD.14 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:S.70, G:S.70, G:R.324, G:S.331, G:D.366, G:G.368, G:G.389, G:S.390, G:S.390, G:Y.413, G:M.416, G:G.417, G:S.418, G:Q.443 IMP.15: 23 residues within 4Å: Chain H: S.70, M.72, R.324, G.330, S.331, I.332, C.333, T.335, D.366, G.367, G.368, M.387, M.388, G.389, S.390, Y.413, G.415, M.416, G.417, S.418, Q.443, G.444 Ligands: NAD.16 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:S.70, H:S.70, H:R.324, H:S.331, H:D.366, H:G.368, H:G.389, H:S.390, H:S.390, H:Y.413, H:M.416, H:G.417, H:S.418, H:Q.443

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

NAD.2: 17 residues within 4Å: Chain A: T.254, R.255, D.276, S.277, S.278, Y.284, N.305, G.326, M.327, G.328, T.335, M.416, G.417, Q.443 Chain D: H.468, Q.471 Ligands: IMP.1 16 PLIP interactions: 3 interactions with chain D, 13 interactions with chain A Hydrogen bonds: D:H.468, D:Q.471, D:Q.471, A:T.254, A:T.254, A:R.255, A:R.255, A:D.276, A:S.278, A:G.326, A:G.328, A:Q.443 pi-Stacking: A:Y.284, A:Y.284 pi-Cation interactions: A:R.255, A:R.255 NAD.4: 17 residues within 4Å: Chain A: H.468, Q.471 Chain B: T.254, R.255, D.276, S.277, S.278, Y.284, N.305, G.326, M.327, G.328, T.335, M.416, G.417, Q.443 Ligands: IMP.3 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.254, B:T.254, B:R.255, B:R.255, B:D.276, B:S.278, B:G.326, B:G.328, B:Q.443, A:H.468, A:Q.471, A:Q.471 pi-Stacking: B:Y.284, B:Y.284 pi-Cation interactions: B:R.255, B:R.255 NAD.6: 17 residues within 4Å: Chain B: H.468, Q.471 Chain C: T.254, R.255, D.276, S.277, S.278, Y.284, N.305, G.326, M.327, G.328, T.335, M.416, G.417, Q.443 Ligands: IMP.5 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:T.254, C:T.254, C:R.255, C:R.255, C:D.276, C:S.278, C:G.326, C:G.328, C:Q.443, B:H.468, B:Q.471, B:Q.471 pi-Stacking: C:Y.284, C:Y.284 pi-Cation interactions: C:R.255, C:R.255 NAD.8: 17 residues within 4Å: Chain C: H.468, Q.471 Chain D: T.254, R.255, D.276, S.277, S.278, Y.284, N.305, G.326, M.327, G.328, T.335, M.416, G.417, Q.443 Ligands: IMP.7 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:T.254, D:T.254, D:R.255, D:R.255, D:D.276, D:S.278, D:G.326, D:G.328, D:Q.443, C:H.468, C:Q.471, C:Q.471 pi-Stacking: D:Y.284, D:Y.284 pi-Cation interactions: D:R.255, D:R.255 NAD.10: 17 residues within 4Å: Chain E: T.254, R.255, D.276, S.277, S.278, Y.284, N.305, G.326, M.327, G.328, T.335, M.416, G.417, Q.443 Chain H: H.468, Q.471 Ligands: IMP.9 15 PLIP interactions: 12 interactions with chain E, 3 interactions with chain H Hydrogen bonds: E:T.254, E:R.255, E:R.255, E:D.276, E:S.278, E:G.326, E:G.328, E:Q.443, H:H.468, H:Q.471, H:Q.471 pi-Stacking: E:Y.284, E:Y.284 pi-Cation interactions: E:R.255, E:R.255 NAD.12: 17 residues within 4Å: Chain E: H.468, Q.471 Chain F: T.254, R.255, D.276, S.277, S.278, Y.284, N.305, G.326, M.327, G.328, T.335, M.416, G.417, Q.443 Ligands: IMP.11 15 PLIP interactions: 12 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:T.254, F:R.255, F:R.255, F:D.276, F:S.278, F:G.326, F:G.328, F:Q.443, E:H.468, E:Q.471, E:Q.471 pi-Stacking: F:Y.284, F:Y.284 pi-Cation interactions: F:R.255, F:R.255 NAD.14: 17 residues within 4Å: Chain F: H.468, Q.471 Chain G: T.254, R.255, D.276, S.277, S.278, Y.284, N.305, G.326, M.327, G.328, T.335, M.416, G.417, Q.443 Ligands: IMP.13 15 PLIP interactions: 12 interactions with chain G, 3 interactions with chain F Hydrogen bonds: G:T.254, G:R.255, G:R.255, G:D.276, G:S.278, G:G.326, G:G.328, G:Q.443, F:H.468, F:Q.471, F:Q.471 pi-Stacking: G:Y.284, G:Y.284 pi-Cation interactions: G:R.255, G:R.255 NAD.16: 17 residues within 4Å: Chain G: H.468, Q.471 Chain H: T.254, R.255, D.276, S.277, S.278, Y.284, N.305, G.326, M.327, G.328, T.335, M.416, G.417, Q.443 Ligands: IMP.15 15 PLIP interactions: 3 interactions with chain G, 12 interactions with chain H Hydrogen bonds: G:H.468, G:Q.471, G:Q.471, H:T.254, H:R.255, H:R.255, H:D.276, H:S.278, H:G.326, H:G.328, H:Q.443 pi-Stacking: H:Y.284, H:Y.284 pi-Cation interactions: H:R.255, H:R.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Calise, S.J. et al., Light-sensitive phosphorylation regulates retinal IMPDH1 activity and filament assembly. J.Cell Biol. (2024)

Release Date

2024-01-31

Peptides

Inosine-5'-monophosphate dehydrogenase 1: 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 1

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