MolNFT v1 · #116745 · protein
Crystal structure of phosphoribosyl isomerase a from streptomyces coelicolor
5DN1: “Crystal structure of phosphoribosyl isomerase a from streptomyces coelicolor”. X-ray diffraction, 2 ligands (AMZ, SO4), 2 pockets (best druggability 0.83). MolNFT v1 #116745 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5DN1
- Type
- protein
- Length
- 240 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosyl isomerase a
- EC
- 5.3.1.16, 5.3.1.24
- UniProt
- P16250
- Ligands
- AMZ, SO4
- Pockets
- 2 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoribosyl isomerase a (EC 5.3.1.16, 5.3.1.24) | protein | 240 | 38% helix, 26% strand | P16250 |
Ligands and binding sites
- AMZ · Aminoimidazole 4-carboxamide ribonucleotide · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.83 | 0.96 | 43 | SO4, AMZ |
| 2 | 55 | 0.55 | 0.89 | 15 | empty |
Compared structures
- 5DN1 · Crystal structure of Phosphoribosyl isomerase A from Streptomyces coelicolor · the same entry in another collection · chain A against A, TM-score 1.00
- P16250 · AlphaFold monomer V2.0 prediction for phosphoribosyl isomerase a (P16250) · a predicted model of the same protein · chain A 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 P16250
- Elsewhere: RCSB PDB 5DN1 · PDBe 5DN1 · UniProt P16250
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