Research workbench
Crystal structure of nicotinate phosphoribosyltransferase (target nysgr-026035) from vibrio cholerae
Analyse Crystal structure of nicotinate phosphoribosyltransferase (target nysgr-026035)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HL7
- Type
- protein
- Length
- 845 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinate phosphoribosyltransferase
- EC
- 2.4.2.11
- UniProt
- Q9KN67
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinate phosphoribosyltransferase (EC 2.4.2.11) | protein | 422 | 50% helix, 16% strand | Q9KN67 |
| B | Nicotinate phosphoribosyltransferase (EC 2.4.2.11) | protein | 423 | 49% helix, 15% strand | Q9KN67 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.73 | 0.83 | 54 | SO4 |
| 2 | 446 | 0.72 | 0.82 | 44 | SO4 |
| 3 | 189 | 0.61 | 0.82 | 29 | empty |
| 4 | 328 | 0.59 | 0.77 | 53 | empty |
| 5 | 106 | 0.46 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 669 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 4HL7 · Crystal structure of nicotinate phosphoribosyltransferase (target NYSGR-026035) from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KN67 · AlphaFold monomer V2.0 prediction for nicotinate phosphoribosyltransferase (Q9KN67) · a predicted model of the same protein · chain B 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 Q9KN67
- Elsewhere: RCSB PDB 4HL7 · PDBe 4HL7 · UniProt Q9KN67
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