Research workbench
Structure of cryptochrome in active conformation
Analyse Structure of cryptochrome in active conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LZ3
- Type
- protein
- Length
- 1,944 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRYPTOCHROME2
- UniProt
- B8A2L5
- Ligands
- FAD
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 1 distinct chain · 42% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | CRYPTOCHROME2 | protein | 486 | 42% helix, 5% strand | B8A2L5 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 674 | 0.83 | 0.87 | 42 | FAD |
| 2 | 659 | 0.83 | 0.87 | 44 | FAD |
| 3 | 648 | 0.83 | 0.87 | 42 | FAD |
| 4 | 679 | 0.82 | 0.86 | 44 | FAD |
| 5 | 139 | 0.80 | 0.97 | 28 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1624 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1596 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1255 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1244 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (flavinylation).
Compared structures
- 6LZ3 · Structure of cryptochrome in active conformation · 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 B8A2L5
- Elsewhere: RCSB PDB 6LZ3 · PDBe 6LZ3 · UniProt B8A2L5
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