MolNFT v1 · #186517 · protein

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

7RGI · Inosine-5'-monophosphate dehydrogenase 1: “Human retinal variant IMPDH1(546) treated with GTP, ATP, imp, NAD+; interface-centered”. Electron microscopy, 2 ligands (NAD, IMP), 20 pockets (best druggability 0.75). MolNFT v1 #186517 on…

PDB: 7RGI
Type: protein
Length: 2,856 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: NAD, IMP
Pockets: 20 · best druggability 0.75

Structure

electron microscopy · 1 distinct chain · 36% helix, 16% 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	357	36% helix, 16% strand	P20839

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, D, B, C, E, H, F, G
IMP · Inosinic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	453	0.75	0.84	72	empty
2	976	0.74	0.77	93	NAD, IMP
3	981	0.74	0.77	90	NAD, IMP
4	945	0.74	0.77	94	NAD, IMP
5	975	0.74	0.77	94	NAD, IMP

Interfaces

16 interfaces between chains.

E–F · 2077 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 2065 Å² buried · 24 hydrogen bonds · protein-protein
A–D · 2065 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 2064 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 2064 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

7RGI · Human retinal variant IMPDH1(546) treated with GTP, ATP, imp, NAD+; interface-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 0.99

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 7RGI · PDBe 7RGI · UniProt P20839

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