Research workbench
1.98 ångström crystal structure of putative 5'-nucleotidase from staphylococcus aureus in complex with adenosine.
Analyse 1.98 ångström crystal structure of putative 5'-nucleotidase from staphylococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q7F
- Type
- protein
- Length
- 510 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5' nucleotidase family protein
- UniProt
- Q5HJM3
- Ligands
- 3D1, MG, MN
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5' nucleotidase family protein | protein | 510 | 30% helix, 29% strand | Q5HJM3 |
Ligands and binding sites
- 3D1 · (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol · ligand · chains A
- MG · Magnesium ion · metal · chains A
- MN · Manganese (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 594 | 0.80 | 0.86 | 64 | 3D1 |
| 2 | 108 | 0.47 | 0.80 | 22 | empty |
| 3 | 54 | 0.29 | 0.75 | 13 | empty |
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 4Q7F · 1.98 Angstrom Crystal Structure of Putative 5'-Nucleotidase from Staphylococcus aureus in… · 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 Q5HJM3
- Elsewhere: RCSB PDB 4Q7F · PDBe 4Q7F · UniProt Q5HJM3
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