MolNFT v1 · #113580 · protein
Crystal structure of ligand-free phosphoribohydrolase lonely guy from claviceps purpurea
5AJT: “Crystal structure of ligand-free phosphoribohydrolase lonely guy from claviceps purpurea”. X-ray diffraction, 3 pockets (best druggability 0.74). MolNFT v1 #113580 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5AJT
- Type
- protein
- Length
- 868 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribohydrolase lonely guy
- UniProt
- M1VUY5
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Phosphoribohydrolase lonely guy | protein | 217 | 47% helix, 18% strand | M1VUY5 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C, D
- TAR · D(-)-tartaric acid · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.74 | 0.78 | 92 | TAR |
| 2 | 385 | 0.64 | 0.78 | 47 | TAR |
| 3 | 362 | 0.62 | 0.78 | 47 | TAR |
Interfaces
4 interfaces between chains.
- A–B · 1593 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1593 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 21 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 17 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5AJT · Crystal structure of ligand-free phosphoribohydrolase lonely guy from Claviceps purpurea · 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 M1VUY5
- Elsewhere: RCSB PDB 5AJT · PDBe 5AJT · UniProt M1VUY5
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