MolNFT v1 · #166257 · protein + DNA
Hhai endonuclease in complex with DNA in space group P41212 (pH 6.0)
6UKH · Hhai restriction endonuclease: “Hhai endonuclease in complex with DNA in space group P41212 (pH 6.0)”. X-ray diffraction, 1 ligand (CA), 4 pockets (best druggability 0.47). MolNFT v1 #166257 on GenesisL1: 3D structure, binding sites…
- 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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