Research workbench
Structure of imp dehydrogenase from ashbya gossypii bound to ATP and GDP
Analyse Structure of imp dehydrogenase from ashbya gossypii bound to ATP and GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TC3
- Type
- protein
- Length
- 977 residues
- Chains
- 2
- 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
- GDP, 5GP, ATP
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 488 | 36% helix, 19% strand | Q756Z6 |
| B | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 489 | 37% helix, 18% strand | Q756Z6 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B
- 5GP · Guanosine-5'-monophosphate · ligand · 2 copies · chains A, B
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 452 | 0.76 | 0.85 | 40 | 5GP |
| 2 | 394 | 0.74 | 0.85 | 41 | 5GP |
| 3 | 822 | 0.73 | 0.78 | 81 | ATP, GDP |
| 4 | 217 | 0.50 | 0.75 | 22 | empty |
| 5 | 83 | 0.43 | 0.80 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1264 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5TC3 · Structure of IMP dehydrogenase from Ashbya gossypii bound to ATP and GDP · 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 5TC3 · PDBe 5TC3 · UniProt Q756Z6
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