Research workbench
Crystal structure of phosphorylated mimic form of human nampt complexed with benzamide and phosphoribosyl pyrophosphate
Analyse Crystal structure of phosphorylated mimic form of human nampt complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DKL
- Type
- protein
- Length
- 928 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
- UNU, BEF, PRP, MG
- Pockets
- 5 · best druggability 0.78
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 | 464 | 41% helix, 19% strand | P43490 |
Ligands and binding sites
- UNU · Benzamide · ligand · 2 copies · chains A, B
- BEF · Beryllium trifluoride ion · ligand · 2 copies · chains A, B
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
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 | 621 | 0.78 | 0.83 | 75 | MG, PRP, UNU, BEF |
| 2 | 687 | 0.78 | 0.83 | 81 | MG, UNU, BEF, PRP |
| 3 | 599 | 0.70 | 0.78 | 54 | empty |
| 4 | 59 | 0.33 | 0.77 | 19 | empty |
| 5 | 50 | 0.29 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 4307 Ų buried · 80 hydrogen bonds · protein-protein
Compared structures
- 3DKL · Crystal structure of phosphorylated mimic form of human NAMPT complexed with benzamide… · 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 3DKL · PDBe 3DKL · UniProt P43490
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