MolNFT v1 · #35079 · protein
Crystal structure of archaeal photolyase from sulfolobus tokodaii with two FAD molecules: implication of a novel light-harvesting cofactor
2E0I · 432AA long hypothetical deoxyribodipyrimidine photolyase: “Crystal structure of archaeal photolyase from sulfolobus tokodaii with two FAD molecules: implication of a…”. X-ray diffraction, 1 ligand (FAD), 14 pockets (best…
- PDB
- 2E0I
- Type
- protein
- Length
- 1,717 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 432AA long hypothetical deoxyribodipyrimidine photolyase
- EC
- 4.1.99.3
- UniProt
- Q973K9
- Ligands
- FAD
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 432AA long hypothetical deoxyribodipyrimidine photolyase (EC 4.1.99.3) | protein | 428 | 51% helix, 7% strand | Q973K9 |
| B | 432AA long hypothetical deoxyribodipyrimidine photolyase (EC 4.1.99.3) | protein | 431 | 51% helix, 7% strand | Q973K9 |
| D | 432AA long hypothetical deoxyribodipyrimidine photolyase (EC 4.1.99.3) | protein | 430 | 51% helix, 7% strand | Q973K9 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.83 | 0.88 | 37 | FAD |
| 2 | 534 | 0.82 | 0.88 | 38 | FAD, MPD |
| 3 | 524 | 0.82 | 0.88 | 37 | FAD, MPD |
| 4 | 533 | 0.82 | 0.87 | 37 | FAD |
| 5 | 437 | 0.80 | 0.88 | 56 | FAD, MPD |
Interfaces
3 interfaces between chains.
- C–D · 943 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 943 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 336 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2E0I · Crystal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules… · 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 Q973K9
- Elsewhere: RCSB PDB 2E0I · PDBe 2E0I · UniProt Q973K9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.