MolNFT v1 · #33269 · protein
Crystal structure of N-((5'-phosphoribosyl)-formimino)-5- aminoimidazol-4-carboxamid ribonucleotid isomerase mutant D127V (ec 3. 1.3.15, hisa)
2CFF · 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)…: “Crystal structure of N-((5'-phosphoribosyl)-formimino)-5- aminoimidazol-4-carboxamid ribonucleotid isomerase…”. X-ray diffraction, 5 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 2CFF
- Type
- protein
- Length
- 482 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino) methylideneamino] imidazole-4-carboxamide…
- EC
- 5.3.1.16
- UniProt
- Q9X0C7
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino) methylideneamino] imidazole-4-carboxamide isomerase (EC 5.3.1.16) | protein | 241 | 42% helix, 24% strand | Q9X0C7 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.79 | 0.85 | 55 | empty |
| 2 | 563 | 0.77 | 0.84 | 49 | MPD |
| 3 | 119 | 0.38 | 0.73 | 17 | empty |
| 4 | 102 | 0.36 | 0.73 | 16 | empty |
| 5 | 72 | 0.30 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 764 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2CFF · Crystal Structure Of N-((5'-Phosphoribosyl)-Formimino)-5- Aminoimidazol-4-Carboxamid… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X0C7 · AlphaFold monomer V2.0 prediction for 1-(5-phosphoribosyl)-5-[(5-PHOSPHORIBOSYLAMINO)METHY… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9X0C7
- Elsewhere: RCSB PDB 2CFF · PDBe 2CFF · UniProt Q9X0C7
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