Research workbench
DNA binding domain of restriction endonuclease bound to DNA
Analyse DNA binding domain of restriction endonuclease bound to DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SSD
- Type
- protein + DNA
- Length
- 327 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-methylcytosine-specific restriction enzyme B; DNA…
- EC
- 3.1.21.-
- UniProt
- P15005
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-methylcytosine-specific restriction enzyme B (EC 3.1.21.-) | protein | 155 | 30% helix, 30% strand | P15005 |
| B | 5-methylcytosine-specific restriction enzyme B (EC 3.1.21.-) | protein | 148 | 29% helix, 26% strand | P15005 |
| C | DNA (5'-D(*T*GP*AP*GP*AP*(5CM)P*CP*GP*GP*TP*AP*GP*C)-3') | dna | 12 | — | — |
| D | DNA (5'-D(*A*GP*CP*TP*AP*CP*CP*GP*GP*TP*CP*TP*C)-3') | dna | 12 | — | — |
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.62 | 0.82 | 25 | empty |
| 2 | 188 | 0.59 | 0.82 | 27 | empty |
| 3 | 460 | 0.57 | 0.74 | 30 | empty |
Interfaces
6 interfaces between chains.
- B–C · 631 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–D · 618 Ų buried · 15 hydrogen bonds · protein-nucleic
- C–D · 509 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- B–D · 342 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–C · 322 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3SSD · DNA binding domain of restriction endonuclease bound to DNA · the same entry in another collection · chain A against A, TM-score 1.00
- P15005 · AlphaFold monomer V2.0 prediction for 5-methylcytosine-specific restriction enzyme B… · 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 P15005
- Elsewhere: RCSB PDB 3SSD · PDBe 3SSD · UniProt P15005
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