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Restriction endonuclease dpni in complex with two DNA molecules
Analyse Restriction endonuclease dpni in complex with two DNA molecules in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KYW
- Type
- protein + DNA
- Length
- 294 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type-2 restriction enzyme dpni; 5'-(*DC*DTP*DGP*DGP*6MAP*DTP*DCP*DCP*DAP*DG)-3'
- EC
- 3.1.21.4
- UniProt
- P0A459
- Ligands
- ZN, CA, NA
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type-2 restriction enzyme dpni (EC 3.1.21.4) | protein | 254 | 34% helix, 23% strand | P0A459 |
| C, D, E, F | 5'-(*DC*DTP*DGP*DGP*6MAP*DTP*DCP*DCP*DAP*DG)-3' | dna | 10 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- CA · Calcium ion · metal · chains A, C
- NA · Sodium ion · metal · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.61 | 0.85 | 29 | empty |
| 2 | 234 | 0.51 | 0.76 | 32 | empty |
| 3 | 76 | 0.32 | 0.74 | 13 | empty |
| 4 | 62 | 0.27 | 0.73 | 11 | empty |
Interfaces
6 interfaces between chains.
- A–C · 860 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–D · 757 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–D · 472 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- E–F · 465 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- A–E · 440 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 4KYW · Restriction endonuclease DPNI in complex with two DNA molecules · the same entry in another collection · chain A against A, TM-score 1.00
- P0A459 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme dpni (P0A459) · a predicted model of the same protein · chain A against A, TM-score 0.71
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 P0A459
- Elsewhere: RCSB PDB 4KYW · PDBe 4KYW · UniProt P0A459
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