MolNFT v2 · #215379 · protein + DNA
SFX structure of the class II photolyase complexed with a thymine dimer
8OET · Deoxyribodipyrimidine photo-lyase: “SFX structure of the class II photolyase complexed with a thymine dimer”. X-ray diffraction at 2.11, 2 ligands (FDA, SO4), 16 pockets (best druggability 0.88). MolNFT v2 #215379 on GenesisL1: 3D…
- PDB
- 8OET
- Type
- protein + DNA
- Length
- 940 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.11
- Source
- Methanosarcina mazei Go1; synthetic construct
- Molecule
- Deoxyribodipyrimidine photo-lyase; DNA (14-mer)
- EC
- 4.1.99.3
- UniProt
- Q8PYK9
- Ligands
- FDA, SO4
- Pockets
- 16 · best druggability 0.88
Structure
x-ray diffraction · resolution 2.11 · 5 distinct chains · 53% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyribodipyrimidine photo-lyase (EC 4.1.99.3) | protein | 457 | 53% helix, 8% strand | Q8PYK9 |
| B | Deoxyribodipyrimidine photo-lyase (EC 4.1.99.3) | protein | 430 | 53% helix, 8% strand | Q8PYK9 |
| C | DNA (14-mer) | dna | 13 | — | — |
| D, F | DNA (14-mer) | dna | 14 | — | — |
| E | DNA (14-mer) | dna | 12 | — | — |
Ligands and binding sites
- FDA · Dihydroflavine-adenine dinucleotide · ligand · 2 copies · chains A, C, B, E
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.88 | 0.90 | 113 | empty |
| 2 | 456 | 0.87 | 0.95 | 46 | FDA |
| 3 | 438 | 0.86 | 0.94 | 45 | FDA |
| 4 | 314 | 0.55 | 0.76 | 22 | empty |
| 5 | 119 | 0.48 | 0.80 | 17 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1210 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 808 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–C · 806 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–D · 624 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–D · 590 Ų buried · 54 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
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 8OET · PDBe 8OET · UniProt Q8PYK9
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