Research workbench
An extraordinary mechanism of DNA perturbation exhibited by the rare- cutting hnh restriction endonuclease paci
Analyse An extraordinary mechanism of DNA perturbation exhibited by the rare- cutting… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LDY
- Type
- protein + DNA
- Length
- 160 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Restriction endonuclease paci; DNA (5'-D(*GP*AP*GP*GP*CP*TP*TP*A)-3'); DNA…
- Ligands
- ZN, CA
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Restriction endonuclease paci | protein | 142 | 42% helix, 13% strand | — |
| B | DNA (5'-D(*GP*AP*GP*GP*CP*TP*TP*A)-3') | dna | 8 | — | — |
| C | DNA (5'-D(P*AP*TP*TP*AP*AP*GP*CP*CP*TP*C)-3') | dna | 10 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.47 | 0.80 | 16 | empty |
| 2 | 59 | 0.30 | 0.75 | 10 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1082 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–B · 582 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–C · 388 Ų buried · 32 hydrogen bonds · nucleic-nucleic
Compared structures
- 3LDY · An extraordinary mechanism of DNA perturbation exhibited by the rare-cutting HNH… · 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
- Elsewhere: RCSB PDB 3LDY · PDBe 3LDY
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