Research workbench
The 5-hydroxymethylcytosine-specific restriction enzyme abasi in a complex with product-like DNA
Analyse The 5-hydroxymethylcytosine-specific restriction enzyme abasi in a complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PAR
- Type
- protein + DNA
- Length
- 1,318 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA 18-mer; DNA 14-mer; Uncharacterized protein abasi
- UniProt
- B0VN39
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F | DNA 18-mer | dna | 18 | — | — |
| G, H | DNA 14-mer | dna | 14 | — | — |
| B, D | Uncharacterized protein abasi | protein | 313 | 27% helix, 31% strand | B0VN39 |
| A | Uncharacterized protein abasi | protein | 314 | 26% helix, 29% strand | B0VN39 |
| C | Uncharacterized protein abasi | protein | 314 | 24% helix, 32% strand | B0VN39 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.83 | 0.88 | 74 | empty |
| 2 | 516 | 0.81 | 0.88 | 67 | empty |
| 3 | 655 | 0.76 | 0.82 | 79 | empty |
| 4 | 441 | 0.72 | 0.82 | 56 | empty |
| 5 | 263 | 0.70 | 0.85 | 46 | empty |
Interfaces
21 interfaces between chains.
- B–A · 1170 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1060 Ų buried · 8 hydrogen bonds · protein-protein
- F–H · 669 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- E–G · 622 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- F–A · 355 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4PAR · The 5-Hydroxymethylcytosine-Specific Restriction Enzyme AbaSI in a Complex with… · the same entry in another collection · chain E against E, 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 B0VN39
- Elsewhere: RCSB PDB 4PAR · PDBe 4PAR · UniProt B0VN39
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