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Crystal structure of a putative nicotinate phosphoribosyltransferase (YOR209C, NPT1) from saccharomyces cerevisiae at 1.75 a resolution
Analyse Crystal structure of a putative nicotinate phosphoribosyltransferase (YOR209C… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VLP
- Type
- protein
- Length
- 1,671 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinate phosphoribosyltransferase
- EC
- 2.4.2.11
- UniProt
- P39683
- Ligands
- PO4, CL
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinate phosphoribosyltransferase (EC 2.4.2.11) | protein | 418 | 46% helix, 18% strand | P39683 |
| B | Nicotinate phosphoribosyltransferase (EC 2.4.2.11) | protein | 419 | 46% helix, 18% strand | P39683 |
| C | Nicotinate phosphoribosyltransferase (EC 2.4.2.11) | protein | 418 | 47% helix, 18% strand | P39683 |
| D | Nicotinate phosphoribosyltransferase (EC 2.4.2.11) | protein | 416 | 48% helix, 17% strand | P39683 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, A, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.84 | 0.85 | 132 | PO4, CL |
| 2 | 529 | 0.79 | 0.85 | 63 | PO4 |
| 3 | 620 | 0.76 | 0.82 | 70 | PO4 |
| 4 | 330 | 0.69 | 0.83 | 49 | PO4 |
| 5 | 234 | 0.62 | 0.81 | 33 | empty |
Interfaces
4 interfaces between chains.
- A–B · 688 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 364 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 14 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 11 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 1VLP · Crystal structure of a putative nicotinate phosphoribosyltransferase (yor209c, npt1) from… · the same entry in another collection · chain D against D, TM-score 1.00
- P39683 · AlphaFold monomer V2.0 prediction for nicotinate phosphoribosyltransferase (P39683) · a predicted model of the same protein · chain D 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 P39683
- Elsewhere: RCSB PDB 1VLP · PDBe 1VLP · UniProt P39683
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