SMTL ID : 7rgl.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

8 x IMP: INOSINIC ACID(Covalent)

IMP.1: 28 residues within 4Å: Chain A: S.68, M.70, N.303, R.322, G.326, G.328, S.329, I.330, C.331, I.332, T.333, D.364, G.365, G.366, I.367, M.385, M.386, G.387, S.388, L.389, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:N.303, A:R.322, A:S.329, A:S.329, A:S.329, A:D.364, A:D.364, A:G.366, A:G.387, A:S.388, A:S.388, A:Y.411, A:M.414, A:G.415, A:S.416, A:Q.441 IMP.3: 28 residues within 4Å: Chain B: S.68, M.70, N.303, R.322, G.326, G.328, S.329, I.330, C.331, I.332, T.333, D.364, G.365, G.366, I.367, M.385, M.386, G.387, S.388, L.389, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.4 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:N.303, B:R.322, B:S.329, B:S.329, B:S.329, B:D.364, B:D.364, B:G.366, B:G.387, B:S.388, B:S.388, B:Y.411, B:M.414, B:G.415, B:S.416, B:Q.441 IMP.5: 28 residues within 4Å: Chain C: S.68, M.70, N.303, R.322, G.326, G.328, S.329, I.330, C.331, I.332, T.333, D.364, G.365, G.366, I.367, M.385, M.386, G.387, S.388, L.389, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.6 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:N.303, C:R.322, C:S.329, C:S.329, C:S.329, C:D.364, C:D.364, C:G.366, C:G.387, C:S.388, C:S.388, C:Y.411, C:M.414, C:G.415, C:S.416, C:Q.441 IMP.7: 29 residues within 4Å: Chain D: S.68, P.69, M.70, N.303, R.322, G.326, G.328, S.329, I.330, C.331, I.332, T.333, D.364, G.365, G.366, I.367, M.385, M.386, G.387, S.388, L.389, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.8 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:N.303, D:R.322, D:S.329, D:S.329, D:S.329, D:D.364, D:D.364, D:G.366, D:G.387, D:S.388, D:S.388, D:Y.411, D:M.414, D:G.415, D:S.416, D:Q.441 IMP.9: 28 residues within 4Å: Chain E: S.68, M.70, N.303, R.322, G.326, G.328, S.329, I.330, C.331, I.332, T.333, D.364, G.365, G.366, I.367, M.385, M.386, G.387, S.388, L.389, 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:N.303, E:R.322, E:S.329, E:S.329, E:D.364, E:D.364, 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: 28 residues within 4Å: Chain F: S.68, M.70, N.303, R.322, G.326, G.328, S.329, I.330, C.331, I.332, T.333, D.364, G.365, G.366, I.367, M.385, M.386, G.387, S.388, L.389, 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:N.303, F:R.322, F:S.329, 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:Y.411, F:M.414, F:G.415, F:S.416, F:Q.441 IMP.13: 29 residues within 4Å: Chain G: S.68, P.69, M.70, N.303, R.322, G.326, G.328, S.329, I.330, C.331, I.332, T.333, D.364, G.365, G.366, I.367, M.385, M.386, G.387, S.388, L.389, 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:N.303, G:R.322, G:S.329, G:S.329, G:D.364, G:D.364, 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: 28 residues within 4Å: Chain H: S.68, P.69, M.70, N.303, R.322, G.326, G.328, S.329, I.330, C.331, I.332, T.333, D.364, G.365, G.366, I.367, M.385, M.386, 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:N.303, H:R.322, H:S.329, H:S.329, H:D.364, H:D.364, 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: 25 residues within 4Å: Chain A: H.93, T.252, R.253, E.254, D.274, S.275, S.276, Q.277, Y.282, N.303, R.322, G.324, M.325, G.326, C.331, T.333, M.414, G.415, Q.441 Chain D: I.42, I.45, A.46, H.466, Q.469 Ligands: IMP.1 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:T.252, A:T.252, A:R.253, A:R.253, A:D.274, A:D.274, A:S.276, A:S.276, A:G.324, A:G.326, A:Q.441, D:Q.469, D:Q.469 pi-Stacking: A:Y.282, A:Y.282 pi-Cation interactions: A:R.253, A:R.253 NAD.4: 25 residues within 4Å: Chain A: I.42, I.45, A.46, H.466, Q.469 Chain B: H.93, T.252, R.253, E.254, D.274, S.275, S.276, Q.277, Y.282, N.303, R.322, G.324, M.325, G.326, C.331, T.333, M.414, G.415, Q.441 Ligands: IMP.3 17 PLIP interactions: 2 interactions with chain A, 15 interactions with chain B Hydrogen bonds: A:Q.469, A:Q.469, B:T.252, B:T.252, B:R.253, B:R.253, B:D.274, B:D.274, B:S.276, B:S.276, B:G.324, B:G.326, B:Q.441 pi-Stacking: B:Y.282, B:Y.282 pi-Cation interactions: B:R.253, B:R.253 NAD.6: 25 residues within 4Å: Chain B: I.42, I.45, A.46, H.466, Q.469 Chain C: H.93, T.252, R.253, E.254, D.274, S.275, S.276, Q.277, Y.282, N.303, R.322, G.324, M.325, G.326, C.331, T.333, M.414, G.415, Q.441 Ligands: IMP.5 18 PLIP interactions: 2 interactions with chain B, 16 interactions with chain C Hydrogen bonds: B:Q.469, B:Q.469, C:T.252, C:T.252, C:R.253, C:R.253, C:D.274, C:D.274, C:S.276, C:S.276, C:Y.282, C:G.324, C:G.326, C:Q.441 pi-Stacking: C:Y.282, C:Y.282 pi-Cation interactions: C:R.253, C:R.253 NAD.8: 25 residues within 4Å: Chain C: I.42, I.45, A.46, H.466, Q.469 Chain D: H.93, T.252, R.253, E.254, D.274, S.275, S.276, Q.277, Y.282, N.303, R.322, G.324, M.325, G.326, C.331, T.333, M.414, G.415, Q.441 Ligands: IMP.7 18 PLIP interactions: 16 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:T.252, D:T.252, D:R.253, D:R.253, D:D.274, D:D.274, D:S.275, D:S.276, D:S.276, D:G.324, D:G.326, D:Q.441, C:Q.469, C:Q.469 pi-Stacking: D:Y.282, D:Y.282 pi-Cation interactions: D:R.253, D:R.253 NAD.10: 25 residues within 4Å: Chain E: H.93, T.252, R.253, E.254, D.274, S.275, S.276, Q.277, Y.282, N.303, R.322, G.324, M.325, G.326, C.331, T.333, M.414, G.415, Q.441 Chain H: I.42, I.45, A.46, H.466, Q.469 Ligands: IMP.9 17 PLIP interactions: 15 interactions with chain E, 2 interactions with chain H Hydrogen bonds: E:T.252, E:T.252, E:R.253, E:R.253, E:D.274, E:D.274, E:S.276, E:S.276, E:Y.282, E:G.324, E:G.326, H:Q.469, H:Q.469 pi-Stacking: E:Y.282, E:Y.282 pi-Cation interactions: E:R.253, E:R.253 NAD.12: 25 residues within 4Å: Chain E: I.42, I.45, A.46, H.466, Q.469 Chain F: H.93, T.252, R.253, E.254, D.274, S.275, S.276, Q.277, Y.282, N.303, R.322, G.324, M.325, G.326, C.331, T.333, M.414, G.415, Q.441 Ligands: IMP.11 19 PLIP interactions: 17 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:T.252, F:T.252, F:R.253, F:R.253, F:D.274, F:D.274, F:S.275, F:S.276, F:S.276, F:Y.282, F:G.324, F:G.326, F:Q.441, E:Q.469, E:Q.469 pi-Stacking: F:Y.282, F:Y.282 pi-Cation interactions: F:R.253, F:R.253 NAD.14: 25 residues within 4Å: Chain F: I.42, I.45, A.46, H.466, Q.469 Chain G: H.93, T.252, R.253, E.254, D.274, S.275, S.276, Q.277, Y.282, N.303, R.322, G.324, M.325, G.326, C.331, T.333, M.414, G.415, Q.441 Ligands: IMP.13 18 PLIP interactions: 16 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:T.252, G:T.252, G:R.253, G:R.253, G:D.274, G:D.274, G:S.276, G:S.276, G:Y.282, G:G.324, G:G.326, G:Q.441, F:Q.469, F:Q.469 pi-Stacking: G:Y.282, G:Y.282 pi-Cation interactions: G:R.253, G:R.253 NAD.16: 25 residues within 4Å: Chain G: I.42, I.45, A.46, H.466, Q.469 Chain H: H.93, T.252, R.253, E.254, D.274, S.275, S.276, Q.277, Y.282, N.303, R.322, G.324, M.325, G.326, C.331, T.333, M.414, G.415, Q.441 Ligands: IMP.15 17 PLIP interactions: 15 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:T.252, H:T.252, H:R.253, H:R.253, H:D.274, H:D.274, H:S.276, H:S.276, H:G.324, H:G.326, H:Q.441, G:Q.469, G:Q.469 pi-Stacking: H:Y.282, H:Y.282 pi-Cation interactions: H:R.253, H:R.253

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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