Research workbench
The 5-hydroxymethylcytosine-specific restriction enzyme abasi in a complex with substrate-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
- 4PBA
- Type
- protein + DNA
- Length
- 1,316 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein abasi; DNA (32-mer)
- UniProt
- B0VN39
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | Uncharacterized protein abasi | protein | 313 | 26% helix, 30% strand | B0VN39 |
| A | Uncharacterized protein abasi | protein | 314 | 25% helix, 30% strand | B0VN39 |
| C | Uncharacterized protein abasi | protein | 314 | 26% helix, 30% strand | B0VN39 |
| E | DNA (32-mer) | dna | 31 | — | — |
| F | DNA (32-mer) | dna | 31 | — | — |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 855 | 0.82 | 0.85 | 75 | empty |
| 2 | 717 | 0.82 | 0.86 | 78 | empty |
| 3 | 749 | 0.77 | 0.82 | 80 | empty |
| 4 | 714 | 0.75 | 0.80 | 82 | empty |
| 5 | 456 | 0.73 | 0.83 | 51 | empty |
Interfaces
12 interfaces between chains.
- E–F · 1398 Ų buried · 115 hydrogen bonds · nucleic-nucleic
- B–A · 1189 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1075 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 380 Ų buried · 5 hydrogen bonds · protein-nucleic
- C–F · 335 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4PBA · The 5-Hydroxymethylcytosine-Specific Restriction Enzyme AbaSI in a Complex with… · the same entry in another collection · chain B against B, 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 4PBA · PDBe 4PBA · UniProt B0VN39
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