Research workbench
Crystal structure of restriction endonuclease ecorii catalytic C- terminal domain in complex with cognate DNA
Analyse Crystal structure of restriction endonuclease ecorii catalytic C- terminal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HQG
- Type
- protein + DNA
- Length
- 246 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type-2 restriction enzyme ecorii; 5'-D(*TP*CP*GP*AP*CP*CP*AP*GP*GP*CP*TP*A)-3'…
- EC
- 3.1.21.4
- UniProt
- P14633
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type-2 restriction enzyme ecorii (EC 3.1.21.4) | protein | 222 | 55% helix, 9% strand | P14633 |
| B | 5'-D(*TP*CP*GP*AP*CP*CP*AP*GP*GP*CP*TP*A)-3' | dna | 12 | — | — |
| C | 5'-D(*TP*AP*GP*CP*CP*TP*GP*GP*TP*CP*GP*A)-3' | dna | 12 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.38 | 0.73 | 17 | GOL |
| 2 | 83 | 0.36 | 0.76 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 816 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–B · 814 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–C · 489 Ų buried · 352 hydrogen bonds · nucleic-nucleic
Compared structures
- 3HQG · Crystal structure of restriction endonuclease EcoRII catalytic C-terminal domain in… · the same entry in another collection · chain A against A, TM-score 1.00
- P14633 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme ecorii (P14633) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 P14633
- Elsewhere: RCSB PDB 3HQG · PDBe 3HQG · UniProt P14633
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