MolNFT v1 · #87859 · protein
Crystal structure of M. mazei photolyase with its in vivo reconstituted 8-hdf antenna chromophore
4CDN · Deoxyribodipyrimidine photolyase: “Crystal structure of M. mazei photolyase with its in vivo reconstituted 8-hdf antenna chromophore”. X-ray diffraction, 3 ligands (FAD, FO1, SO4), 14 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 4CDN
- Type
- protein
- Length
- 901 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyribodipyrimidine photolyase
- EC
- 4.1.99.3
- UniProt
- Q8PYK9
- Ligands
- FAD, FO1, SO4
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyribodipyrimidine photolyase (EC 4.1.99.3) | protein | 463 | 51% helix, 7% strand | Q8PYK9 |
| B | Deoxyribodipyrimidine photolyase (EC 4.1.99.3) | protein | 438 | 52% helix, 7% strand | Q8PYK9 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- FO1 · 1-deoxy-1-(8-hydroxy-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-D-ribitol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 582 | 0.83 | 0.88 | 38 | FAD, GOL |
| 2 | 564 | 0.83 | 0.88 | 44 | FAD, GOL |
| 3 | 147 | 0.81 | 0.97 | 30 | FO1 |
| 4 | 135 | 0.80 | 0.97 | 24 | FO1 |
| 5 | 1141 | 0.72 | 0.75 | 111 | PGE |
Interfaces
1 interface between chains.
- A–B · 455 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4CDN · Crystal structure of M. mazei photolyase with its in vivo reconstituted 8-HDF antenna… · 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 4CDN · PDBe 4CDN · UniProt Q8PYK9
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