Research workbench
Crystal structure of nicotinic acid mononucleotide adenylyltransferase from staphylococcus aureus: product bound form 2
Analyse Crystal structure of nicotinic acid mononucleotide adenylyltransferase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H2A
- Type
- protein
- Length
- 378 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable nicotinate-nucleotide adenylyltransferase
- EC
- 2.7.7.18
- UniProt
- Q5HFG7
- Ligands
- DND, CA
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable nicotinate-nucleotide adenylyltransferase (EC 2.7.7.18) | protein | 189 | 41% helix, 20% strand | Q5HFG7 |
Ligands and binding sites
- DND · Nicotinic acid adenine dinucleotide · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 378 | 0.78 | 0.88 | 54 | DND |
| 2 | 399 | 0.77 | 0.86 | 57 | DND |
| 3 | 173 | 0.65 | 0.85 | 23 | empty |
| 4 | 75 | 0.33 | 0.75 | 12 | empty |
| 5 | 61 | 0.30 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1052 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 2H2A · Crystal structure of Nicotinic acid mononucleotide adenylyltransferase from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5HFG7 · AlphaFold monomer V2.0 prediction for probable nicotinate-nucleotide adenylyltransferase… · a predicted model of the same protein · chain A 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 Q5HFG7
- Elsewhere: RCSB PDB 2H2A · PDBe 2H2A · UniProt Q5HFG7
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