MolNFT v1 · #189507 · protein
Class II photolyase mmcpdii oxidized to semiquinone tr-sfx studies (10 us time-point)
7VJ1 · DNA photolyase: “Class II photolyase mmcpdii oxidized to semiquinone tr-sfx studies (10 us time-point)”. X-ray diffraction, 2 ligands (FAD, SO4), 4 pockets (best druggability 0.84). MolNFT v1 #189507 on GenesisL1: 3D structure…
- PDB
- 7VJ1
- 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, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA photolyase (EC 4.1.99.3) | protein | 450 | 51% helix, 7% 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 | 559 | 0.84 | 0.89 | 47 | SO4, FAD |
| 2 | 383 | 0.81 | 0.90 | 42 | empty |
| 3 | 122 | 0.43 | 0.76 | 23 | empty |
| 4 | 78 | 0.40 | 0.78 | 16 | empty |
Compared structures
- 7VJ1 · class II photolyase MmCPDII oxidized to semiqui TR-SFX studies (10 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 7VJ1 · PDBe 7VJ1 · UniProt Q8PYK9
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