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Structure of imp dehydrogenase from ashbya gossypii bound to ATP

Analyse Structure of imp dehydrogenase from ashbya gossypii bound to ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MCP
Type: protein
Length: 3,205 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Inosine-5'-monophosphate dehydrogenase
EC: 1.1.1.205
UniProt: Q756Z6
Ligands: ATP, MG
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 8 distinct chains · 39% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205)	protein	440	36% helix, 19% strand	Q756Z6
B	Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205)	protein	444	38% helix, 19% strand	Q756Z6
C	Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205)	protein	446	38% helix, 19% strand	Q756Z6
D	Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205)	protein	443	38% helix, 19% strand	Q756Z6
E	Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205)	protein	387	40% helix, 13% strand	Q756Z6
F	Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205)	protein	342	42% helix, 12% strand	Q756Z6
G	Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205)	protein	382	41% helix, 14% strand	Q756Z6
H	Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205)	protein	321	42% helix, 10% strand	Q756Z6

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 24 copies · chains A, E, B, F, C, H, D, G
MG · Magnesium ion · metal · 8 copies · chains B, C, H, D, A, E, 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	493	0.78	0.86	44	empty
2	515	0.72	0.81	77	empty
3	126	0.72	0.92	40	empty
4	576	0.69	0.78	57	empty
5	132	0.69	0.90	32	empty

Interfaces

12 interfaces between chains.

A–D · 1910 Å² buried · 35 hydrogen bonds · protein-protein
B–C · 1888 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 1867 Å² buried · 28 hydrogen bonds · protein-protein
C–D · 1856 Å² buried · 29 hydrogen bonds · protein-protein
E–F · 1431 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

5MCP · Structure of IMP dehydrogenase from Ashbya gossypii bound to ATP · the same entry in another collection · chain A against A, TM-score 1.00

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 Q756Z6
Elsewhere: RCSB PDB 5MCP · PDBe 5MCP · UniProt Q756Z6

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