SMTL ID : 7rgi.1

HUMAN RETINAL VARIANT IMPDH1(546) TREATED WITH GTP, ATP, IMP, NAD+; INTERFACE-CENTERED

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

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

NAD.1: 19 residues within 4Å: Chain A: P.69, M.70, H.93, T.252, R.253, E.254, D.274, S.275, S.276, S.280, Y.282, N.303, R.322, Q.441 Chain D: I.42, I.45, A.46, Q.469 Ligands: IMP.2 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:P.69, A:H.93, A:T.252, A:R.253, A:E.254, A:D.274, A:S.276, A:S.276, A:S.276, A:S.280, A:R.322, A:R.322, A:Q.441, D:Q.469, D:Q.469 pi-Stacking: A:Y.282 pi-Cation interactions: A:R.253, A:R.253 NAD.3: 19 residues within 4Å: Chain A: I.42, I.45, A.46, H.466, Q.469 Chain B: P.69, M.70, H.93, T.252, R.253, E.254, D.274, S.275, S.276, Y.282, N.303, R.322, Q.441 Ligands: IMP.4 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:P.69, B:H.93, B:T.252, B:R.253, B:D.274, B:S.276, B:S.276, B:S.276, B:R.322, B:R.322, B:Q.441, A:Q.469, A:Q.469 pi-Stacking: B:Y.282 pi-Cation interactions: B:R.253, B:R.253 NAD.5: 20 residues within 4Å: Chain B: I.42, I.45, A.46, H.466, Q.469 Chain C: P.69, M.70, H.93, T.252, R.253, E.254, D.274, S.275, S.276, S.280, Y.282, N.303, R.322, Q.441 Ligands: IMP.6 16 PLIP interactions: 14 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:P.69, C:H.93, C:T.252, C:R.253, C:D.274, C:S.276, C:S.276, C:S.276, C:R.322, C:R.322, C:Q.441, B:Q.469, B:Q.469 pi-Stacking: C:Y.282 pi-Cation interactions: C:R.253, C:R.253 NAD.7: 21 residues within 4Å: Chain C: I.42, I.45, A.46, H.466, Q.469 Chain D: P.69, M.70, H.93, T.252, R.253, E.254, D.274, S.275, S.276, Q.277, S.280, Y.282, N.303, R.322, Q.441 Ligands: IMP.8 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:H.93, D:T.252, D:R.253, D:D.274, D:S.276, D:S.276, D:N.303, D:Q.441, C:Q.469, C:Q.469 pi-Stacking: D:Y.282 pi-Cation interactions: D:R.253, D:R.253 NAD.9: 20 residues within 4Å: Chain E: S.68, P.69, M.70, H.93, T.252, R.253, E.254, D.274, S.275, S.276, Y.282, N.303, R.322, Q.441 Chain H: I.42, I.45, A.46, H.466, Q.469 Ligands: IMP.10 16 PLIP interactions: 14 interactions with chain E, 2 interactions with chain H Hydrogen bonds: E:P.69, E:H.93, E:T.252, E:R.253, E:D.274, E:S.276, E:S.276, E:S.276, E:R.322, E:R.322, E:Q.441, H:Q.469, H:Q.469 pi-Stacking: E:Y.282 pi-Cation interactions: E:R.253, E:R.253 NAD.11: 20 residues within 4Å: Chain E: I.42, I.45, A.46, H.466, Q.469 Chain F: P.69, M.70, H.93, T.252, R.253, E.254, D.274, S.275, S.276, Q.277, Y.282, N.303, R.322, Q.441 Ligands: IMP.12 16 PLIP interactions: 14 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:P.69, F:H.93, F:T.252, F:R.253, F:D.274, F:S.276, F:S.276, F:S.276, F:R.322, F:R.322, F:Q.441, E:Q.469, E:Q.469 pi-Stacking: F:Y.282 pi-Cation interactions: F:R.253, F:R.253 NAD.13: 20 residues within 4Å: Chain F: I.42, I.45, A.46, H.466, Q.469 Chain G: P.69, M.70, H.93, T.252, R.253, E.254, D.274, S.275, S.276, S.280, Y.282, N.303, R.322, Q.441 Ligands: IMP.14 17 PLIP interactions: 15 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:P.69, G:H.93, G:T.252, G:R.253, G:E.254, G:D.274, G:S.276, G:S.276, G:S.276, G:R.322, G:R.322, G:Q.441, F:Q.469, F:Q.469 pi-Stacking: G:Y.282 pi-Cation interactions: G:R.253, G:R.253 NAD.15: 20 residues within 4Å: Chain G: I.42, I.45, A.46, H.466, Q.469 Chain H: P.69, M.70, H.93, T.252, R.253, E.254, D.274, S.275, S.276, S.280, Y.282, N.303, R.322, Q.441 Ligands: IMP.16 17 PLIP interactions: 14 interactions with chain H, 3 interactions with chain G Hydrogen bonds: H:P.69, H:H.93, H:T.252, H:R.253, H:D.274, H:S.276, H:S.276, H:S.276, H:R.322, H:R.322, H:Q.441, G:H.466, G:Q.469, G:Q.469 pi-Stacking: H:Y.282 pi-Cation interactions: H:R.253, H:R.253

8 x IMP: INOSINIC ACID(Non-covalent)

IMP.2: 21 residues within 4Å: Chain A: S.68, M.70, S.276, N.303, R.322, C.327, G.328, S.329, I.330, C.331, T.333, D.364, G.365, G.366, I.367, M.386, G.387, S.388, Q.441, G.442 Ligands: NAD.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.329, A:D.364, A:D.364, A:G.366, A:G.387, A:S.388 IMP.4: 22 residues within 4Å: Chain B: S.68, P.69, M.70, S.276, N.303, R.322, G.328, S.329, I.330, C.331, T.333, D.364, G.365, G.366, I.367, M.385, M.386, G.387, S.388, Q.441, G.442 Ligands: NAD.3 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.68, B:N.303, B:R.322, B:S.329, B:D.364, B:D.364, B:G.366, B:G.387, B:S.388, B:S.388, B:Q.441 IMP.6: 22 residues within 4Å: Chain C: S.68, M.70, S.276, N.303, R.322, C.327, G.328, S.329, I.330, C.331, T.333, D.364, G.365, G.366, I.367, M.385, M.386, G.387, S.388, Q.441, G.442 Ligands: NAD.5 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:S.68, C:N.303, C:R.322, C:S.329, C:D.364, C:D.364, C:G.366, C:G.387, C:S.388, C:Q.441 IMP.8: 22 residues within 4Å: Chain D: S.68, M.70, S.276, N.303, R.322, G.328, S.329, I.330, C.331, T.333, D.364, G.365, G.366, I.367, M.385, M.386, G.387, S.388, L.389, Q.441, G.442 Ligands: NAD.7 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:S.68, D:N.303, D:R.322, D:S.329, D:D.364, D:D.364, D:G.366, D:G.387, D:S.388, D:Q.441 IMP.10: 22 residues within 4Å: Chain E: S.68, P.69, M.70, S.276, N.303, R.322, G.326, G.328, S.329, I.330, C.331, T.333, D.364, G.365, G.366, I.367, M.385, G.387, S.388, Q.441, G.442 Ligands: NAD.9 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:S.68, E:N.303, E:R.322, E:S.329, E:I.330, E:D.364, E:D.364, E:G.366, E:I.367, E:S.388, E:S.388, E:S.388 IMP.12: 22 residues within 4Å: Chain F: S.68, P.69, M.70, S.276, N.303, R.322, G.328, S.329, I.330, C.331, T.333, D.364, G.365, G.366, I.367, M.385, M.386, G.387, S.388, Q.441, G.442 Ligands: NAD.11 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:S.68, F:N.303, F:R.322, F:S.329, F:D.364, F:D.364, F:G.366, F:G.387, F:S.388, F:S.388, F:S.388, F:Q.441 IMP.14: 21 residues within 4Å: Chain G: S.68, P.69, M.70, S.276, N.303, R.322, G.328, S.329, I.330, C.331, T.333, D.364, G.365, G.366, I.367, M.385, G.387, S.388, Q.441, G.442 Ligands: NAD.13 13 PLIP interactions: 13 interactions with chain G Hydrogen bonds: G:S.68, G:N.303, G:R.322, G:S.329, G:I.330, G:D.364, G:D.364, G:G.366, G:I.367, G:G.387, G:S.388, G:S.388, G:S.388 IMP.16: 22 residues within 4Å: Chain H: S.68, P.69, M.70, S.276, N.303, R.322, G.326, G.328, S.329, I.330, C.331, T.333, D.364, G.365, G.366, I.367, M.385, G.387, S.388, Q.441, G.442 Ligands: NAD.15 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:S.68, H:N.303, H:R.322, H:S.329, H:I.330, H:D.364, H:D.364, H:G.366, H:I.367, H:S.388, H:S.388, H:S.388

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burrell, A.L. et al., IMPDH1 retinal variants control filament architecture to tune allosteric regulation. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-01-12

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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