Research workbench

Human IMPDH1 treated with ATP, imp, and NAD+

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

PDB: 7RER
Type: protein
Length: 3,112 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Isoform 5 of inosine-5'-monophosphate dehydrogenase 1
EC: 1.1.1.205
UniProt: P20839
Ligands: NAD, IMP
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 1 distinct chain · 35% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, C, B, E, H, G, F	Isoform 5 of inosine-5'-monophosphate dehydrogenase 1 (EC 1.1.1.205)	protein	389	35% helix, 19% strand	P20839

Ligands and binding sites

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

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	1012	0.80	0.81	85	NAD, IMP
2	997	0.80	0.81	78	NAD, IMP
3	985	0.79	0.81	87	NAD, IMP
4	699	0.79	0.84	42	empty
5	1068	0.79	0.81	91	NAD, IMP

Interfaces

16 interfaces between chains.

D–C · 2431 Å² buried · 42 hydrogen bonds · protein-protein
C–B · 2429 Å² buried · 41 hydrogen bonds · protein-protein
A–B · 2421 Å² buried · 41 hydrogen bonds · protein-protein
E–F · 2419 Å² buried · 40 hydrogen bonds · protein-protein
A–D · 2404 Å² buried · 44 hydrogen bonds · protein-protein

Compared structures

7RER · Human IMPDH1 treated with ATP, imp, and NAD+ · the same entry in another collection · chain F against F, 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 0.96

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 7RER · PDBe 7RER · UniProt P20839

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