MolNFT v1 · #164819 · protein
Human nampt deletion mutant in complex with nicotinamide mononucleotide, pyrophosphate, and MG2+
6TAC · Nicotinamide phosphoribosyltransferase: “Human nampt deletion mutant in complex with nicotinamide mononucleotide, pyrophosphate, and MG2+”. X-ray diffraction, 3 ligands (NMN, PPV, MG), 5 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 6TAC
- Type
- protein
- Length
- 934 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinamide phosphoribosyltransferase
- EC
- 2.4.2.12
- UniProt
- P43490
- Ligands
- NMN, PPV, MG
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 467 | 41% helix, 19% strand | P43490 |
Ligands and binding sites
- NMN · Beta-nicotinamide ribose monophosphate · ligand · 2 copies · chains A, B
- PPV · Pyrophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- GOL · Glycerol · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 695 | 0.79 | 0.84 | 83 | MG, NMN, PPV |
| 2 | 723 | 0.78 | 0.82 | 80 | MG, PPV, NMN |
| 3 | 663 | 0.72 | 0.79 | 51 | empty |
| 4 | 63 | 0.33 | 0.77 | 17 | empty |
| 5 | 53 | 0.31 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 4280 Ų buried · 74 hydrogen bonds · protein-protein
Compared structures
- 6TAC · Human NAMPT deletion mutant in complex with nicotinamide mononucleotide, pyrophosphate… · 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 P43490
- Elsewhere: RCSB PDB 6TAC · PDBe 6TAC · UniProt P43490
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