MolNFT v1 · #170899 · protein + DNA
VCAM4I restriction endonuclease in complex with 5MC-modified dsdna
6YMG · Hnh endonuclease: “VCAM4I restriction endonuclease in complex with 5MC-modified dsdna”. X-ray diffraction, 2 ligands (SO4, CL), 9 pockets (best druggability 0.80). MolNFT v1 #170899 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6YMG
- Type
- protein + DNA
- Length
- 662 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hnh endonuclease; DNA (5'-D(*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*A)-3'); DNA…
- UniProt
- A0A344KQF3
- Ligands
- SO4, CL
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hnh endonuclease | protein | 309 | 39% helix, 18% strand | A0A344KQF3 |
| C, E | DNA (5'-D(*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*A)-3') | dna | 11 | — | — |
| D, F | DNA (5'-D(P*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3') | dna | 11 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1130 | 0.80 | 0.81 | 86 | SO4 |
| 2 | 97 | 0.62 | 0.89 | 19 | empty |
| 3 | 122 | 0.61 | 0.87 | 21 | empty |
| 4 | 273 | 0.55 | 0.77 | 23 | empty |
| 5 | 183 | 0.45 | 0.75 | 23 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2345 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 797 Ų buried · 27 hydrogen bonds · protein-nucleic
- B–E · 794 Ų buried · 26 hydrogen bonds · protein-nucleic
- E–F · 524 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- C–D · 523 Ų buried · 44 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6YMG · VcaM4I restriction endonuclease in complex with 5mC-modified dsDNA · 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 6YMG · PDBe 6YMG · UniProt A0A344KQF3
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