Research workbench
Crystal structure of a bifunctional nmn ADENYLYLTRANSFERASE/ADP ribose pyrophosphatase (nadm) complexed with adprp and NAD from synechocystis sp.
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
- 2QJO
- Type
- protein
- Length
- 995 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional nmn ADENYLYLTRANSFERASE/NUDIX hydrolase
- EC
- 2.7.7.1, 3.6.1.-
- UniProt
- Q55928
- Ligands
- APR, NAD, POP, SO4
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional nmn ADENYLYLTRANSFERASE/NUDIX hydrolase (EC 2.7.7.1, 3.6.1.-) | protein | 332 | 38% helix, 23% strand | Q55928 |
| B | Bifunctional nmn ADENYLYLTRANSFERASE/NUDIX hydrolase (EC 2.7.7.1, 3.6.1.-) | protein | 336 | 39% helix, 23% strand | Q55928 |
| C | Bifunctional nmn ADENYLYLTRANSFERASE/NUDIX hydrolase (EC 2.7.7.1, 3.6.1.-) | protein | 327 | 38% helix, 23% strand | Q55928 |
Ligands and binding sites
- APR · Adenosine-5-diphosphoribose · ligand · 3 copies · chains A, C, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, B, C
- POP · Pyrophosphate 2- · ligand · 3 copies · chains A, B, C
- 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
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.83 | 0.84 | 118 | NAD, POP |
| 2 | 965 | 0.82 | 0.83 | 86 | NAD, POP |
| 3 | 928 | 0.82 | 0.83 | 80 | NAD, POP |
| 4 | 248 | 0.63 | 0.81 | 50 | APR |
| 5 | 216 | 0.54 | 0.78 | 32 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1153 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 970 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2QJO · crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose pyrophosphatase… · the same entry in another collection · chain C against C, TM-score 1.00
- Q55928 · AlphaFold monomer V2.0 prediction for bifunctional nmn ADENYLYLTRANSFERASE/NUDIX… · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q55928
- Elsewhere: RCSB PDB 2QJO · PDBe 2QJO · UniProt Q55928
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