MolNFT v1 · #28944 · protein
Crystal structure of a nicotinate phosphoribosyltransferase from thermoplasma acidophilum with nicotinate mononucleotide
1YTK: “Crystal structure of a nicotinate phosphoribosyltransferase from thermoplasma acidophilum with nicotinate…”. X-ray diffraction, 1 ligand (NCN), 3 pockets (best druggability 0.50). MolNFT v1 #28944 on GenesisL1: 3D structure, binding…
- PDB
- 1YTK
- Type
- protein
- Length
- 389 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinate phosphoribosyltransferase from thermoplasma acidophilum
- EC
- 2.4.2.11
- UniProt
- Q9HJ28
- Ligands
- NCN
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinate phosphoribosyltransferase from thermoplasma acidophilum (EC 2.4.2.11) | protein | 389 | 40% helix, 21% strand | Q9HJ28 |
Ligands and binding sites
- NCN · Nicotinate mononucleotide · ligand · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.50 | 0.75 | 26 | empty |
| 2 | 142 | 0.42 | 0.75 | 22 | NCN |
| 3 | 112 | 0.42 | 0.76 | 20 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1YTK · Crystal structure of a nicotinate phosphoribosyltransferase from Thermoplasma acidophilum… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HJ28 · AlphaFold monomer V2.0 prediction for putative nicotinate phosphoribosyltransferase… · 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 Q9HJ28
- Elsewhere: RCSB PDB 1YTK · PDBe 1YTK · UniProt Q9HJ28
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