MolNFT v1 · #189514 · protein
Sfx structure of archaeal class II cpd photolyase from methanosarcina mazei in the oxidized state
7VJ8 · DNA photolyase: “Sfx structure of archaeal class II cpd photolyase from methanosarcina mazei in the oxidized state”. X-ray diffraction, 2 ligands (FAD, SO4), 4 pockets (best druggability 0.84). MolNFT v1 #189514 on GenesisL1: 3D…
- PDB
- 7VJ8
- Type
- protein
- Length
- 453 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA photolyase
- EC
- 4.1.99.3
- UniProt
- Q8PYK9
- Ligands
- FAD, SO4
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA photolyase (EC 4.1.99.3) | protein | 453 | 52% helix, 8% strand | Q8PYK9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 552 | 0.84 | 0.90 | 42 | FAD |
| 2 | 397 | 0.79 | 0.88 | 40 | empty |
| 3 | 76 | 0.49 | 0.83 | 23 | SO4 |
| 4 | 79 | 0.39 | 0.78 | 15 | empty |
Compared structures
- 7VJ8 · SFX structure of archaeal class II CPD photolyase from Methanosarcina mazei in the… · 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 Q8PYK9
- Elsewhere: RCSB PDB 7VJ8 · PDBe 7VJ8 · UniProt Q8PYK9
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