MolNFT v1 · #168854 · protein

Sort-tagged drosophila cryptochrome

6WTB · Cryptochrome-1: “Sort-tagged drosophila cryptochrome”. X-ray diffraction, 2 ligands (FAD, MG), 12 pockets (best druggability 0.85). MolNFT v1 #168854 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6WTB
Type: protein
Length: 1,084 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cryptochrome-1
UniProt: O77059
Ligands: FAD, MG
Pockets: 12 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cryptochrome-1	protein	537	49% helix, 7% strand	O77059
B	Cryptochrome-1	protein	547	48% helix, 6% strand	O77059

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 3 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	904	0.85	0.87	68	MG, FAD
2	1087	0.85	0.85	89	MG, FAD
3	412	0.79	0.88	43	MG
4	372	0.70	0.83	42	empty
5	138	0.51	0.80	25	empty

Interfaces

1 interface between chains.

A–B · 1088 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6WTB · Sort-Tagged Drosophila Cryptochrome · the same entry in another collection · chain A against A, TM-score 1.00
O77059 · AlphaFold monomer V2.0 prediction for cryptochrome-1 (O77059) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 O77059
Elsewhere: RCSB PDB 6WTB · PDBe 6WTB · UniProt O77059

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