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Crystal structure of type I restriction enzyme ecoki M protein (ec 2.1.1.72) (M.ECOKI)
Analyse Crystal structure of type I restriction enzyme ecoki M protein (ec 2.1.1.72)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AR0
- Type
- protein
- Length
- 968 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type I restriction enzyme ecoki M protein
- EC
- 2.1.1.72
- UniProt
- P08957
- Ligands
- UNX
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type I restriction enzyme ecoki M protein (EC 2.1.1.72) | protein | 485 | 43% helix, 13% strand | P08957 |
| B | Type I restriction enzyme ecoki M protein (EC 2.1.1.72) | protein | 483 | 42% helix, 13% strand | P08957 |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 10 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 779 | 0.71 | 0.77 | 72 | empty |
| 2 | 134 | 0.57 | 0.83 | 38 | empty |
| 3 | 157 | 0.48 | 0.77 | 27 | empty |
| 4 | 79 | 0.46 | 0.81 | 23 | empty |
| 5 | 139 | 0.45 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 512 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 2AR0 · Crystal structure of Type I restriction enzyme EcoKI M protein (EC 2.1.1.72) (M.EcoKI) · the same entry in another collection · chain A against A, TM-score 1.00
- P08957 · AlphaFold monomer V2.0 prediction for type I restriction enzyme ecoki M protein (P08957) · a predicted model of the same protein · chain B against A, TM-score 0.68
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 P08957
- Elsewhere: RCSB PDB 2AR0 · PDBe 2AR0 · UniProt P08957
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