Research workbench
Crystal structure of a bifunctional nmn ADENYLYLTRANSFERASE/ADP ribose pyrophosphatase complexed with AMP and mn ion from francisella tularensis
Analyse Crystal structure of a bifunctional nmn ADENYLYLTRANSFERASE/ADP ribose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QJT
- Type
- protein
- Length
- 684 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinamide-nucleotide adenylyltransferase
- EC
- 2.7.7.1, 3.6.1.-
- UniProt
- Q5NHR1
- Ligands
- AMP, MN
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Nicotinamide-nucleotide adenylyltransferase (EC 2.7.7.1, 3.6.1.-) | protein | 344 | 36% helix, 24% strand | Q5NHR1 |
| A | Nicotinamide-nucleotide adenylyltransferase (EC 2.7.7.1, 3.6.1.-) | protein | 340 | 34% helix, 24% strand | Q5NHR1 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains B, A
- MN · Manganese (II) ion · metal · 9 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.71 | 0.78 | 75 | empty |
| 2 | 658 | 0.70 | 0.78 | 69 | empty |
| 3 | 296 | 0.69 | 0.84 | 50 | AMP, MN |
| 4 | 127 | 0.55 | 0.83 | 33 | MN, AMP |
| 5 | 276 | 0.50 | 0.74 | 30 | empty |
Interfaces
1 interface between chains.
- B–A · 1083 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2QJT · Crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose pyrophosphatase… · the same entry in another collection · chain B against B, 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 Q5NHR1
- Elsewhere: RCSB PDB 2QJT · PDBe 2QJT · UniProt Q5NHR1
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