Research workbench
Crystal structure of deoxyribonucleotidase-like protein (NP_764060.1) from staphylococcus epidermidis atcc 12228 at 1.55 a resolution
Analyse Crystal structure of deoxyribonucleotidase-like protein (NP_764060.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BWV
- Type
- protein
- Length
- 335 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative 5'(3')-deoxyribonucleotidase
- EC
- 3.1.3.-
- UniProt
- Q8CTG7
- Ligands
- MG, CL
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative 5'(3')-deoxyribonucleotidase (EC 3.1.3.-) | protein | 167 | 43% helix, 18% strand | Q8CTG7 |
| B | Putative 5'(3')-deoxyribonucleotidase (EC 3.1.3.-) | protein | 168 | 41% helix, 18% strand | Q8CTG7 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.58 | 0.78 | 33 | MG |
| 2 | 225 | 0.49 | 0.75 | 35 | empty |
| 3 | 109 | 0.43 | 0.77 | 23 | CL |
| 4 | 63 | 0.32 | 0.76 | 15 | empty |
| 5 | 52 | 0.27 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1029 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 3BWV · Crystal structure of deoxyribonucleotidase-like protein (NP_764060.1) from Staphylococcus… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8CTG7 · AlphaFold monomer V2.0 prediction for putative 5'(3')-deoxyribonucleotidase (Q8CTG7) · a predicted model of the same protein · chain B 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 Q8CTG7
- Elsewhere: RCSB PDB 3BWV · PDBe 3BWV · UniProt Q8CTG7
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