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Human retinal variant IMPDH1(546) treated with ATP, imp, NAD+, octamer-centered

Analyse Human retinal variant IMPDH1(546) treated with ATP, imp, NAD+, octamer-centered in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7RGM
Type: protein
Length: 3,872 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Inosine-5'-monophosphate dehydrogenase 1
EC: 1.1.1.205
UniProt: P20839
Ligands: ATP, IMP, NAD
Pockets: 20 · best druggability 0.78

Structure

electron microscopy · 1 distinct chain · 32% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Inosine-5'-monophosphate dehydrogenase 1 (EC 1.1.1.205)	protein	484	32% helix, 20% strand	P20839

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 16 copies · chains A, H, B, G, C, F, D, E
IMP · Inosinic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, D, B, C, E, H, F, G

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	941	0.78	0.81	78	IMP, NAD
2	963	0.78	0.80	77	IMP, NAD
3	934	0.77	0.80	79	IMP, NAD
4	1106	0.77	0.79	105	IMP, NAD
5	776	0.77	0.81	60	IMP, NAD

Interfaces

12 interfaces between chains.

E–F · 2239 Å² buried · 32 hydrogen bonds · protein-protein
E–H · 2238 Å² buried · 31 hydrogen bonds · protein-protein
A–B · 2220 Å² buried · 34 hydrogen bonds · protein-protein
F–G · 2216 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 2195 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

7RGM · Human retinal variant IMPDH1(546) treated with ATP, imp, NAD+, octamer-centered · the same entry in another collection · chain H against H, TM-score 1.00
P20839 · AlphaFold monomer V2.0 prediction for inosine-5'-monophosphate dehydrogenase 1 (P20839) · a predicted model of the same protein · chain A against A, TM-score 0.87

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P20839
Elsewhere: RCSB PDB 7RGM · PDBe 7RGM · UniProt P20839

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