Research workbench
Sfx structure of archaeal class II cpd photolyase from methanosarcina mazei in the semiquinone state
Analyse Sfx structure of archaeal class II cpd photolyase from methanosarcina mazei in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VJ6
- 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 0.83
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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 551 | 0.83 | 0.89 | 44 | FAD |
| 2 | 380 | 0.79 | 0.88 | 37 | empty |
| 3 | 71 | 0.51 | 0.85 | 24 | SO4 |
| 4 | 86 | 0.39 | 0.77 | 23 | empty |
Compared structures
- 7VJ6 · 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 7VJ6 · PDBe 7VJ6 · UniProt Q8PYK9
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