MolNFT v1 · #148995 · protein + DNA
The animal-like cryptochrome from chlamydomonas reinhardtii in complex with 6-4 DNA
6FN0 · Cryptochrome photoreceptor: “The animal-like cryptochrome from chlamydomonas reinhardtii in complex with 6-4 DNA”. X-ray diffraction, 3 ligands (FAD, MG, CL), 6 pockets (best druggability 0.86). MolNFT v1 #148995 on GenesisL1: 3D…
- PDB
- 6FN0
- Type
- protein + DNA
- Length
- 524 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cryptochrome photoreceptor; DNA (5'-D(*CP*AP*GP*CP*GP*GP*(64T)P*(5PY)…
- UniProt
- A8J8W0
- Ligands
- FAD, MG, CL
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cryptochrome photoreceptor | protein | 496 | 48% helix, 6% strand | A8J8W0 |
| C | DNA (5'-D(*CP*AP*GP*CP*GP*GP*(64T)P*(5PY) P*GP*CP*CP*GP*TP*G)-3') | dna | 14 | — | — |
| D | DNA (5'-D(*CP*AP*CP*GP*GP*CP*AP*AP*CP*CP*GP*CP*TP*G)-3') | dna | 14 | — | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains C
- CL · Chloride ion · ion · chains D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
- GOL · Glycerol · additive · chains A
- 1PE · Pentaethylene glycol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.86 | 0.96 | 34 | FAD |
| 2 | 531 | 0.75 | 0.82 | 39 | MES |
| 3 | 274 | 0.69 | 0.85 | 37 | empty |
| 4 | 146 | 0.47 | 0.78 | 17 | empty |
| 5 | 92 | 0.33 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 775 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–D · 587 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–D · 571 Ų buried · 55 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6FN0 · The animal-like Cryptochrome from Chlamydomonas reinhardtii in complex with 6-4 DNA · the same entry in another collection · chain C against C, 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 A8J8W0
- Elsewhere: RCSB PDB 6FN0 · PDBe 6FN0 · UniProt A8J8W0
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