Research workbench
Alteration of sequence specificity of the type II restriction endonuclease hincii through an indirect readout mechanism
Analyse Alteration of sequence specificity of the type II restriction endonuclease… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GIG
- Type
- protein + DNA
- Length
- 517 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*GP*C)-3'; Type II restriction enzyme hincii
- EC
- 3.1.21.4
- UniProt
- P44413
- Ligands
- NA
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F | 5'-D(*GP*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*GP*C)-3' | dna | 14 | — | — |
| A | Type II restriction enzyme hincii (EC 3.1.21.4) | protein | 249 | 43% helix, 23% strand | P44413 |
| B | Type II restriction enzyme hincii (EC 3.1.21.4) | protein | 240 | 43% helix, 23% strand | P44413 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains F, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 734 | 0.71 | 0.78 | 54 | empty |
| 2 | 426 | 0.70 | 0.82 | 30 | empty |
| 3 | 211 | 0.58 | 0.80 | 34 | empty |
| 4 | 268 | 0.56 | 0.77 | 33 | empty |
| 5 | 106 | 0.46 | 0.80 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1295 Ų buried · 8 hydrogen bonds · protein-protein
- F–A · 961 Ų buried · 23 hydrogen bonds · protein-nucleic
- E–A · 708 Ų buried · 15 hydrogen bonds · protein-nucleic
- E–B · 666 Ų buried · 13 hydrogen bonds · protein-nucleic
- E–F · 653 Ų buried · 52 hydrogen bonds · nucleic-nucleic
Compared structures
- 2GIG · Alteration of sequence specificity of the type II restriction endonuclease HINCII through… · the same entry in another collection · chain E against E, TM-score 1.00
- P44413 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme hindii (P44413) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P44413
- Elsewhere: RCSB PDB 2GIG · PDBe 2GIG · UniProt P44413
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