Research workbench
Crystal structure of enterococcus faecalis nicotinate phosphoribosyltransferase with malonate and phosphate bound
Analyse Crystal structure of enterococcus faecalis nicotinate phosphoribosyltransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MZY
- Type
- protein
- Length
- 486 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinate phosphoribosyltransferase
- EC
- 2.4.2.11
- UniProt
- Q830Y8
- Ligands
- CL, PO4
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinate phosphoribosyltransferase (EC 2.4.2.11) | protein | 486 | 42% helix, 20% strand | Q830Y8 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 12 copies · chains A
- MLA · Malonic acid · additive · 3 copies · chains A
- FMT · Formic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.67 | 0.81 | 43 | GOL, MLA |
| 2 | 253 | 0.56 | 0.77 | 32 | PO4, FMT, CL |
| 3 | 121 | 0.47 | 0.78 | 23 | empty |
| 4 | 149 | 0.45 | 0.76 | 21 | GOL |
| 5 | 74 | 0.41 | 0.80 | 16 | empty |
Compared structures
- 4MZY · Crystal structure of enterococcus faecalis nicotinate phosphoribosyltransferase with… · 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 Q830Y8
- Elsewhere: RCSB PDB 4MZY · PDBe 4MZY · UniProt Q830Y8
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