Research workbench
VCAM4I restriction endonuclease in the presence of 5MC-modified ssdna
Analyse VCAM4I restriction endonuclease in the presence of 5MC-modified ssdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YKF
- Type
- protein + DNA
- Length
- 314 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hnh endonuclease; DNA (5'-D(*CP*AP*(5CM)P*AP*G)-3')
- UniProt
- A0A344KQF3
- Ligands
- SO4, CL
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hnh endonuclease | protein | 309 | 40% helix, 19% strand | A0A344KQF3 |
| B | DNA (5'-D(*CP*AP*(5CM)P*AP*G)-3') | dna | 5 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 11 copies · chains A, B
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.59 | 0.78 | 33 | SO4 |
| 2 | 73 | 0.33 | 0.75 | 12 | GOL |
| 3 | 64 | 0.27 | 0.72 | 15 | empty |
| 4 | 50 | 0.25 | 0.74 | 12 | GOL |
Interfaces
1 interface between chains.
- A–B · 736 Ų buried · 19 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent, 1 modified (additive adduct, nucleotide modification).
Compared structures
- 6YKF · VcaM4I restriction endonuclease in the presence of 5mC-modified ssDNA · the same entry in another collection · chain A against A, 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 A0A344KQF3
- Elsewhere: RCSB PDB 6YKF · PDBe 6YKF · UniProt A0A344KQF3
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