MolNFT v1 · #37973 · protein + DNA
Alteration of sequence specificity of the type II restriction endonuclease hincii through an indirect readout mechanism
2GIG · 5'-D(*GP*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*GP*C)-3': “Alteration of sequence specificity of the type II restriction endonuclease hincii through an indirect readout…”. X-ray diffraction, 1 ligand (NA), 8 pockets (best druggability…
- 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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