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Restriction endonuclease dpni in complex with target DNA
Analyse Restriction endonuclease dpni in complex with target DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ESJ
- Type
- protein + DNA
- Length
- 523 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type-2 restriction enzyme dpni; DNA (5'-D(*CP*TP*GP*GP*(6MA)P*TP*CP*CP*AP*G)-3')
- EC
- 3.1.21.4
- UniProt
- P0A460
- Ligands
- ZN, UNX, AZI
- Pockets
- 6 · best druggability 0.42
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type-2 restriction enzyme dpni (EC 3.1.21.4) | protein | 246 | 39% helix, 27% strand | P0A460 |
| B | Type-2 restriction enzyme dpni (EC 3.1.21.4) | protein | 241 | 40% helix, 24% strand | P0A460 |
| C, D | DNA (5'-D(*CP*TP*GP*GP*(6MA)P*TP*CP*CP*AP*G)-3') | dna | 10 | — | — |
| E | DNA (5'-D(*CP*TP*GP*GP*(6MA)P*TP*CP*CP*AP*G)-3') | dna | 8 | — | — |
| F | DNA (5'-D(*CP*TP*GP*GP*(6MA)P*TP*CP*CP*AP*G)-3') | dna | 8 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B
- UNX · Unknown atom or ion · ion · 2 copies · chains C, D
- AZI · Azide ion · ion · chains A
- GOL · Glycerol · additive · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.42 | 0.77 | 21 | empty |
| 2 | 133 | 0.41 | 0.75 | 23 | empty |
| 3 | 74 | 0.38 | 0.78 | 15 | empty |
| 4 | 59 | 0.38 | 0.79 | 10 | empty |
| 5 | 62 | 0.38 | 0.79 | 18 | empty |
Interfaces
7 interfaces between chains.
- C–D · 470 Ų buried · 32 hydrogen bonds · nucleic-nucleic
- A–D · 467 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–E · 401 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–C · 388 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–F · 388 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
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 P0A460
- Elsewhere: RCSB PDB 4ESJ · PDBe 4ESJ · UniProt P0A460
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