Research workbench
Structural insights into catalytic and substrate binding mechanisms of the strategic enda nuclease from streptococcus pneumoniae
Analyse Structural insights into catalytic and substrate binding mechanisms of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OWV
- Type
- protein
- Length
- 442 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-entry nuclease
- EC
- 3.1.30.-
- UniProt
- P0A3S3
- Ligands
- MG, CL
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-entry nuclease (EC 3.1.30.-) | protein | 218 | 17% helix, 32% strand | P0A3S3 |
| B | DNA-entry nuclease (EC 3.1.30.-) | protein | 224 | 17% helix, 32% strand | P0A3S3 |
Ligands and binding sites
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 | 747 | 0.72 | 0.78 | 48 | empty |
| 2 | 83 | 0.34 | 0.75 | 20 | MG, CL |
| 3 | 59 | 0.29 | 0.75 | 19 | MG, CL |
Interfaces
1 interface between chains.
- A–B · 542 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3OWV · Structural insights into catalytic and substrate binding mechanisms of the strategic EndA… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A3S3 · AlphaFold monomer V2.0 prediction for DNA-entry nuclease (P0A3S3) · a predicted model of the same protein · 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 P0A3S3
- Elsewhere: RCSB PDB 3OWV · PDBe 3OWV · UniProt P0A3S3
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