Research workbench
Class II photolyase mmcpdii oxidized to semiquinone tr-sfx studies (125 us time-point)
Analyse Class II photolyase mmcpdii oxidized to semiquinone tr-sfx studies (125 us… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VJ2
- Type
- protein
- Length
- 448 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, NA, 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 | 448 | 52% helix, 8% strand | Q8PYK9 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
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 | 532 | 0.84 | 0.90 | 39 | FAD |
| 2 | 430 | 0.79 | 0.87 | 45 | empty |
| 3 | 68 | 0.44 | 0.82 | 18 | empty |
| 4 | 90 | 0.39 | 0.77 | 19 | empty |
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 7VJ2 · class II photolyase MmCPDII oxidized to semiqui TR-SFX studies (125 us 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 7VJ2 · PDBe 7VJ2 · UniProt Q8PYK9
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