MolNFT v1 · #37677 · protein
Crystal structure of VISFATIN/PRE-B cell colony enhancing factor 1/NICOTINAMIDE phosphoribosyltransferase in complex with niconamide mononucleotide
2G96: “Crystal structure of VISFATIN/PRE-B cell colony enhancing factor 1/NICOTINAMIDE phosphoribosyltransferase in…”. X-ray diffraction, 1 ligand (NMN), 4 pockets (best druggability 0.79). MolNFT v1 #37677 on GenesisL1: 3D structure…
- PDB
- 2G96
- Type
- protein
- Length
- 926 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinamide phosphoribosyltransferase
- EC
- 2.4.2.12
- UniProt
- Q80Z29
- Ligands
- NMN
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 463 | 38% helix, 20% strand | Q80Z29 |
Ligands and binding sites
- NMN · Beta-nicotinamide ribose monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 795 | 0.79 | 0.83 | 89 | NMN |
| 2 | 633 | 0.76 | 0.82 | 77 | NMN |
| 3 | 473 | 0.68 | 0.79 | 41 | empty |
| 4 | 58 | 0.31 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 4250 Ų buried · 94 hydrogen bonds · protein-protein
Compared structures
- 2G96 · Crystal Structure of Visfatin/Pre-B Cell Colony Enhancing Factor 1/Nicotinamide… · the same entry in another collection · chain A against A, TM-score 1.00
- Q80Z29 · AlphaFold monomer V2.0 prediction for nicotinamide phosphoribosyltransferase (Q80Z29) · a predicted model of the same protein · 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 Q80Z29
- Elsewhere: RCSB PDB 2G96 · PDBe 2G96 · UniProt Q80Z29
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