MolNFT v1 · #74228 · protein + DNA
Restriction endonuclease HPY188I in complex with substrate DNA
3OQG: “Restriction endonuclease HPY188I in complex with substrate DNA”. X-ray diffraction, 2 ligands (NA, CL), 1 pocket (best druggability 0.83). MolNFT v1 #74228 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3OQG
- Type
- protein + DNA
- Length
- 369 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HPY188I; DNA 5'-D(*GP*AP*TP*CP*TP*GP*AP*AP*C)-3'; DNA 5'-D(*GP*TP*TP*CP*AP*GP*AP*TP*C)-3'
- UniProt
- Q9KJ88
- Ligands
- NA, CL
- Pockets
- 1 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HPY188I | protein | 176 | 34% helix, 26% strand | Q9KJ88 |
| B | HPY188I | protein | 175 | 36% helix, 26% strand | Q9KJ88 |
| C | DNA 5'-D(*GP*AP*TP*CP*TP*GP*AP*AP*C)-3' | dna | 9 | — | — |
| D | DNA 5'-D(*GP*TP*TP*CP*AP*GP*AP*TP*C)-3' | dna | 9 | — | — |
Ligands and binding sites
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 | 220 | 0.83 | 0.96 | 38 | NA |
Interfaces
6 interfaces between chains.
- A–B · 2543 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 779 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–C · 763 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–D · 488 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 479 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 3OQG · Restriction endonuclease HPY188I in complex with substrate 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 3OQG · PDBe 3OQG · UniProt Q9KJ88
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