Research workbench
Crystal structure of nadr protein in complex with NAD and AMP-pnp
Analyse Crystal structure of nadr protein in complex with NAD and AMP-pnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GZO
- Type
- protein
- Length
- 711 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinamide-nucleotide adenylyltransferase nadr family / ribosylnicotinamide kinase
- UniProt
- A0A165F602
- Ligands
- ANP, NAD, PO4
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinamide-nucleotide adenylyltransferase nadr family / ribosylnicotinamide kinase | protein | 355 | 50% helix, 14% strand | A0A165F602 |
| B | Nicotinamide-nucleotide adenylyltransferase nadr family / ribosylnicotinamide kinase | protein | 356 | 49% helix, 15% strand | A0A165F602 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.71 | 0.81 | 57 | empty |
| 2 | 275 | 0.62 | 0.80 | 29 | PO4 |
| 3 | 252 | 0.57 | 0.78 | 25 | empty |
| 4 | 95 | 0.53 | 0.84 | 18 | ANP |
| 5 | 149 | 0.49 | 0.78 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 2323 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 6GZO · Crystal structure of NadR protein in complex with NAD and AMP-PNP · 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 6GZO · PDBe 6GZO · UniProt A0A165F602
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