Research workbench
Crystal structure of NadR protein in complex with NR
Analyse Crystal structure of NadR protein in complex with NR in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GYF
- Type
- protein
- Length
- 727 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Lactococcus lactis subsp. cremoris
- Molecule
- Nicotinamide-nucleotide adenylyltransferase NadR family / Ribosylnicotinamide kinase
- UniProt
- A0A165F602
- Ligands
- NMN, MG, SO4
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · resolution 2.7 · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinamide-nucleotide adenylyltransferase NadR family / Ribosylnicotinamide kinase | protein | 361 | 48% helix, 16% strand | A0A165F602 |
| B | Nicotinamide-nucleotide adenylyltransferase NadR family / Ribosylnicotinamide kinase | protein | 366 | 47% helix, 16% strand | A0A165F602 |
Ligands and binding sites
- NMN · Beta-nicotinamide ribose monophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.72 | 0.81 | 67 | empty |
| 2 | 247 | 0.65 | 0.83 | 30 | SO4 |
| 3 | 302 | 0.63 | 0.80 | 34 | SO4 |
| 4 | 250 | 0.57 | 0.78 | 26 | empty |
| 5 | 110 | 0.54 | 0.83 | 19 | NMN |
Interfaces
1 interface between chains.
- A–B · 2412 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 6GYF · Crystal structure of nadr protein in complex with nr · 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 A0A165F602
- Elsewhere: RCSB PDB 6GYF · PDBe 6GYF · UniProt A0A165F602
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