Research workbench
Crystal structure of human nmprtase and its complex with nmn
Analyse Crystal structure of human nmprtase and its complex with nmn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GVG
- Type
- protein
- Length
- 2,777 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinamide phosphoribosyltransferase
- EC
- 2.4.2.12
- UniProt
- P43490
- Ligands
- NMN, PO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 461 | 40% helix, 18% strand | P43490 |
| B, D, E | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 464 | 39% helix, 19% strand | P43490 |
| F | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 463 | 39% helix, 19% strand | P43490 |
Ligands and binding sites
- NMN · Beta-nicotinamide ribose monophosphate · ligand · 6 copies · chains A, C, B, D, E, F
- PO4 · Phosphate ion · ion · 12 copies · chains A, C, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.79 | 0.84 | 76 | PO4, NMN |
| 2 | 747 | 0.79 | 0.83 | 82 | PO4, NMN |
| 3 | 736 | 0.79 | 0.83 | 80 | PO4, NMN |
| 4 | 760 | 0.78 | 0.82 | 78 | PO4, NMN |
| 5 | 568 | 0.70 | 0.79 | 52 | empty |
Interfaces
8 interfaces between chains.
- A–C · 4235 Ų buried · 72 hydrogen bonds · protein-protein
- D–E · 4216 Ų buried · 73 hydrogen bonds · protein-protein
- C–E · 528 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 501 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 252 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2GVG · Crystal Structure of human NMPRTase and its complex with NMN · 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 2GVG · PDBe 2GVG · UniProt P43490
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