Research workbench
Crystal structure of nuca from streptococcus agalactiae with no metal bound
Analyse Crystal structure of nuca from streptococcus agalactiae with no metal bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QGO
- Type
- protein
- Length
- 429 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-entry nuclease (competence-specific nuclease)
- UniProt
- R5A2Y6
- Ligands
- SO4, CL
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-entry nuclease (competence-specific nuclease) | protein | 215 | 18% helix, 29% strand | R5A2Y6 |
| B | DNA-entry nuclease (competence-specific nuclease) | protein | 214 | 17% helix, 29% strand | R5A2Y6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 563 | 0.67 | 0.77 | 46 | empty |
| 2 | 115 | 0.40 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 427 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4QGO · Crystal structure of NucA from Streptococcus agalactiae with no metal bound · 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 R5A2Y6
- Elsewhere: RCSB PDB 4QGO · PDBe 4QGO · UniProt R5A2Y6
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