Research workbench
Hhai endonuclease in complex with DNA in space group P41212 (pH 6.0)
Analyse Hhai endonuclease in complex with DNA in space group P41212 (pH 6.0) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UKH
- Type
- protein + DNA
- Length
- 284 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hhai restriction endonuclease; DNA (5'-D(*CP*TP*GP*TP*TP*GP*CP*GP*CP*TP*TP*GP*G)-3'); DNA…
- EC
- 3.-.-.-
- UniProt
- I3DBY6
- Ligands
- CA
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Hhai restriction endonuclease (EC 3.-.-.-) | protein | 258 | 29% helix, 34% strand | I3DBY6 |
| A | DNA (5'-D(*CP*TP*GP*TP*TP*GP*CP*GP*CP*TP*TP*GP*G)-3') | dna | 13 | — | — |
| B | DNA (5'-D(*CP*CP*AP*AP*GP*CP*GP*CP*AP*AP*CP*AP*G)-3') | dna | 13 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains X, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.47 | 0.78 | 18 | empty |
| 2 | 204 | 0.47 | 0.75 | 21 | empty |
| 3 | 183 | 0.45 | 0.75 | 22 | empty |
| 4 | 87 | 0.35 | 0.75 | 13 | empty |
Interfaces
3 interfaces between chains.
- X–A · 1226 Ų buried · 26 hydrogen bonds · protein-nucleic
- X–B · 766 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–B · 619 Ų buried · 58 hydrogen bonds · nucleic-nucleic
Compared structures
- 6UKH · HhaI endonuclease in Complex with DNA in space group P41212 (pH 6.0) · the same entry in another collection · chain X against X, 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 I3DBY6
- Elsewhere: RCSB PDB 6UKH · PDBe 6UKH · UniProt I3DBY6
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