MolNFT v1 · #166254 · protein + DNA
Hhai endonuclease in complex with iodine-labelled DNA
6UKE · Hhai restriction endonuclease: “Hhai endonuclease in complex with iodine-labelled DNA”. X-ray diffraction, 2 ligands (CA, PO4), 3 pockets (best druggability 0.61). MolNFT v1 #166254 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6UKE
- 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(*TP*CP*CP*AP*AP*GP*CP*GP*CP*AP*AP*CP*G)-3'); DNA…
- EC
- 3.-.-.-
- UniProt
- I3DBY6
- Ligands
- CA, PO4
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Hhai restriction endonuclease (EC 3.-.-.-) | protein | 258 | 30% helix, 33% strand | I3DBY6 |
| A | DNA (5'-D(*TP*CP*CP*AP*AP*GP*CP*GP*CP*AP*AP*CP*G)-3') | dna | 13 | — | — |
| B | DNA (5'-D(*CP*GP*(5IT)P*TP*GP*CP*GP*CP*TP*(5IT)P*GP*GP*A)- 3') | dna | 13 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · chains X
- PO4 · Phosphate ion · ion · chains X
- EDO · 1,2-ethanediol · additive · 19 copies · chains X, B, A
- ACT · Acetate ion · additive · 2 copies · chains X, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 363 | 0.61 | 0.78 | 35 | EDO |
| 2 | 158 | 0.44 | 0.75 | 26 | CA, EDO |
| 3 | 89 | 0.36 | 0.75 | 13 | empty |
Interfaces
3 interfaces between chains.
- X–A · 1181 Ų buried · 29 hydrogen bonds · protein-nucleic
- X–B · 804 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–B · 626 Ų buried · 53 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6UKE · HhaI endonuclease in Complex with Iodine-Labelled DNA · 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 6UKE · PDBe 6UKE · UniProt I3DBY6
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