Research workbench
Crystal structure of a nicotinate phosphoribosyltransferase
Analyse Crystal structure of a nicotinate phosphoribosyltransferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YIR
- Type
- protein
- Length
- 1,560 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinate phosphoribosyltransferase 2
- EC
- 2.4.2.11
- UniProt
- Q9HW26
- Ligands
- SO4
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Nicotinate phosphoribosyltransferase 2 (EC 2.4.2.11) | protein | 390 | 50% helix, 17% strand | Q9HW26 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 821 | 0.76 | 0.80 | 95 | SO4 |
| 2 | 743 | 0.76 | 0.80 | 81 | SO4 |
| 3 | 527 | 0.74 | 0.82 | 47 | SO4 |
| 4 | 424 | 0.72 | 0.83 | 48 | SO4 |
| 5 | 411 | 0.63 | 0.78 | 44 | SO4 |
Interfaces
3 interfaces between chains.
- A–C · 612 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 404 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 302 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1YIR · Crystal Structure of a Nicotinate Phosphoribosyltransferase · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HW26 · AlphaFold monomer V2.0 prediction for nicotinate phosphoribosyltransferase 2 (Q9HW26) · 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 Q9HW26
- Elsewhere: RCSB PDB 1YIR · PDBe 1YIR · UniProt Q9HW26
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.