Research workbench
Crystal structure of type II restrcition endonuclease, ECOO109I complexed with cognate DNA
Analyse Crystal structure of type II restrcition endonuclease, ECOO109I complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WTE
- Type
- protein + DNA
- Length
- 570 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*CP*CP*GP*GP*GP*CP*CP*CP*TP*GP*CP*C)-3'…
- EC
- 3.1.21.4
- UniProt
- Q9RPJ3
- Ligands
- NA
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | 5'-D(*AP*CP*CP*GP*GP*GP*CP*CP*CP*TP*GP*CP*C)-3' | dna | 13 | — | — |
| Y | 5'-D(*GP*GP*CP*AP*GP*GP*GP*CP*CP*CP*GP*GP*T)-3' | dna | 13 | — | — |
| A, B | ECOO109IR (EC 3.1.21.4) | protein | 272 | 54% helix, 10% strand | Q9RPJ3 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains X, A, Y, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.78 | 0.98 | 18 | empty |
| 2 | 59 | 0.73 | 0.98 | 16 | empty |
| 3 | 455 | 0.66 | 0.78 | 36 | empty |
| 4 | 385 | 0.64 | 0.79 | 40 | empty |
| 5 | 413 | 0.64 | 0.78 | 37 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3545 Ų buried · 40 hydrogen bonds · protein-protein
- X–B · 929 Ų buried · 19 hydrogen bonds · protein-nucleic
- Y–A · 909 Ų buried · 19 hydrogen bonds · protein-nucleic
- X–A · 687 Ų buried · 12 hydrogen bonds · protein-nucleic
- Y–B · 676 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 1WTE · Crystal structure of type II restrcition endonuclease, EcoO109I complexed with cognate 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 Q9RPJ3
- Elsewhere: RCSB PDB 1WTE · PDBe 1WTE · UniProt Q9RPJ3
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