MolNFT v1 · #33750 · protein
Crystal structure of inosine-5'-monophosphate dehydrogenase from pyrococcus horikoshii OT3
2CU0: “Crystal structure of inosine-5'-monophosphate dehydrogenase from pyrococcus horikoshii OT3”. X-ray diffraction, 1 ligand (XMP), 10 pockets (best druggability 0.80). MolNFT v1 #33750 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2CU0
- Type
- protein
- Length
- 713 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
- O58045
- Ligands
- XMP
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 358 | 33% helix, 20% strand | O58045 |
| B | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 355 | 34% helix, 21% strand | O58045 |
Ligands and binding sites
- XMP · Xanthosine-5'-monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.80 | 0.87 | 57 | XMP |
| 2 | 491 | 0.78 | 0.86 | 51 | XMP |
| 3 | 390 | 0.60 | 0.76 | 31 | empty |
| 4 | 251 | 0.51 | 0.75 | 20 | empty |
| 5 | 161 | 0.44 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 745 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2CU0 · Crystal structure of inosine-5'-monophosphate dehydrogenase from Pyrococcus horikoshii OT3 · the same entry in another collection · chain A against A, TM-score 1.00
- O58045 · AlphaFold monomer V2.0 prediction for inosine-5'-monophosphate dehydrogenase (O58045) · a predicted model of the same protein · chain B 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 O58045
- Elsewhere: RCSB PDB 2CU0 · PDBe 2CU0 · UniProt O58045
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