MolNFT v1 · #59137 · protein
Crystal structure of a putative DNA replication regulator hda (SAMA_1916) from shewanella amazonensis SB2B at 1.75 a resolution
3BOS · Putative DNA replication factor: “Crystal structure of a putative DNA replication regulator hda (SAMA_1916) from shewanella amazonensis SB2B at…”. X-ray diffraction, 5 ligands (CDP, MG, NA), 3 pockets (best druggability 0.79).…
- PDB
- 3BOS
- Type
- protein
- Length
- 459 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative DNA replication factor
- UniProt
- A1S6W5
- Ligands
- CDP, MG, NA, SCN, CL
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative DNA replication factor | protein | 228 | 52% helix, 12% strand | A1S6W5 |
| B | Putative DNA replication factor | protein | 231 | 51% helix, 12% strand | A1S6W5 |
Ligands and binding sites
- CDP · Cytidine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- SCN · Thiocyanate ion · ion · chains A
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 861 | 0.79 | 0.82 | 95 | MG, CDP, EDO |
| 2 | 153 | 0.51 | 0.80 | 21 | EDO |
| 3 | 169 | 0.49 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2063 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3BOS · Crystal structure of a putative dna replication regulator HDA (SAMA_1916) from Shewanella… · 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 A1S6W5
- Elsewhere: RCSB PDB 3BOS · PDBe 3BOS · UniProt A1S6W5
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