MolNFT v1 · #102115 · protein
DNA modification-dependent restriction endonuclease aspbhi
4OC8: “DNA modification-dependent restriction endonuclease aspbhi”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.85). MolNFT v1 #102115 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4OC8
- Type
- protein
- Length
- 1,204 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Restriction endonuclease aspbhi
- UniProt
- A1K2B7
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Restriction endonuclease aspbhi | protein | 387 | 29% helix, 28% strand | A1K2B7 |
| C, D | Restriction endonuclease aspbhi | protein | 215 | 20% helix, 32% strand | A1K2B7 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.85 | 0.87 | 93 | empty |
| 2 | 880 | 0.85 | 0.87 | 74 | empty |
| 3 | 444 | 0.77 | 0.86 | 63 | empty |
| 4 | 268 | 0.69 | 0.84 | 28 | empty |
| 5 | 62 | 0.52 | 0.87 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3097 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 714 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 712 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 432 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 406 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4OC8 · DNA modification-dependent restriction endonuclease AspBHI · 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 A1K2B7
- Elsewhere: RCSB PDB 4OC8 · PDBe 4OC8 · UniProt A1K2B7
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