Research workbench
Crystal structure of type iip restriction endonuclease pfoi with cognate DNA
Analyse Crystal structure of type iip restriction endonuclease pfoi with cognate DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EKO
- Type
- protein + DNA
- Length
- 652 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Restriction endonuclease pfoi; DNA (5'-D(*CP*GP*CP*TP*CP*CP*CP*GP*GP*AP*GP*CP*GP*T)-3')
- EC
- 3.1.21.4
- Ligands
- CA
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Restriction endonuclease pfoi (EC 3.1.21.4) | protein | 312 | 40% helix, 17% strand | — |
| F, E | DNA (5'-D(*CP*GP*CP*TP*CP*CP*CP*GP*GP*AP*GP*CP*GP*T)-3') | dna | 14 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, F, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 390 | 0.76 | 0.86 | 35 | empty |
| 2 | 455 | 0.75 | 0.84 | 38 | empty |
| 3 | 170 | 0.63 | 0.85 | 33 | empty |
| 4 | 64 | 0.46 | 0.84 | 14 | empty |
| 5 | 57 | 0.44 | 0.84 | 13 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2264 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 1164 Ų buried · 32 hydrogen bonds · protein-nucleic
- B–F · 1141 Ų buried · 33 hydrogen bonds · protein-nucleic
- B–E · 903 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–F · 891 Ų buried · 21 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 18 modified (engineered, artifact).
Compared structures
- 6EKO · Crystal structure of Type IIP restriction endonuclease PfoI with cognate DNA · 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 6EKO · PDBe 6EKO
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