MolNFT v1 · #134677 · protein
Structure of imp dehydrogenase from ashbya gossypii bound to ATP and GDP
5TC3 · Inosine-5'-monophosphate dehydrogenase: “Structure of imp dehydrogenase from ashbya gossypii bound to ATP and GDP”. X-ray diffraction, 3 ligands (GDP, 5GP, ATP), 11 pockets (best druggability 0.76). MolNFT v1 #134677 on GenesisL1…
- 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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