Research workbench
Restriction endonuclease HPY188I in complex with product DNA
Analyse Restriction endonuclease HPY188I in complex with product DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OR3
- Type
- protein + DNA
- Length
- 364 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Restriction endonuclease HPY188I; 5'-D(*GP*AP*TP*CP*T)-3'; 5'-D(*GP*TP*TP*CP*A)-3'…
- UniProt
- Q9KJ88
- Ligands
- CA, CL
- Pockets
- 1 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Restriction endonuclease HPY188I | protein | 173 | 35% helix, 25% strand | Q9KJ88 |
| C | 5'-D(*GP*AP*TP*CP*T)-3' | dna | 5 | — | — |
| D | 5'-D(*GP*TP*TP*CP*A)-3' | dna | 5 | — | — |
| E | 5'-D(P*GP*AP*AP*C)-3' | dna | 4 | — | — |
| F | 5'-D(P*GP*AP*TP*C)-3' | dna | 4 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, D, F, C, E
- CL · Chloride ion · ion · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 386 | 0.80 | 0.90 | 49 | CA, CL |
Interfaces
13 interfaces between chains.
- A–B · 2622 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 568 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–E · 550 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–D · 479 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–C · 441 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 3OR3 · Restriction endonuclease HPY188I in complex with product DNA · 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 Q9KJ88
- Elsewhere: RCSB PDB 3OR3 · PDBe 3OR3 · UniProt Q9KJ88
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