Research workbench
Class II photolyase mmcpdii oxidized to semiquinone tr-sfx studies (10 ns time-point)
Analyse Class II photolyase mmcpdii oxidized to semiquinone tr-sfx studies (10 ns… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VIX
- Type
- protein
- Length
- 450 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 · 51% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA photolyase (EC 4.1.99.3) | protein | 450 | 51% 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 | 534 | 0.84 | 0.90 | 40 | FAD |
| 2 | 381 | 0.77 | 0.87 | 40 | empty |
| 3 | 96 | 0.42 | 0.78 | 20 | empty |
| 4 | 61 | 0.31 | 0.75 | 17 | empty |
Compared structures
- 7VIX · class II photolyase MmCPDII oxidized to semiqui TR-SFX studies (10 ns time-point) · 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 7VIX · PDBe 7VIX · UniProt Q8PYK9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.