MolNFT v1 · #169144 · protein

Structural basis of plant blue light photoreceptor

6X24 · Cryptochrome-2: “Structural basis of plant blue light photoreceptor”. X-ray diffraction, 1 ligand (FAD), 20 pockets (best druggability 0.85). MolNFT v1 #169144 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6X24
Type: protein
Length: 1,879 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cryptochrome-2
UniProt: Q96524
Ligands: FAD
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cryptochrome-2	protein	469	49% helix, 5% strand	Q96524
C	Cryptochrome-2	protein	471	49% helix, 5% strand	Q96524
D	Cryptochrome-2	protein	470	50% helix, 6% strand	Q96524

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 15 copies · chains A, B, D, C

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	498	0.85	0.92	45	GOL
2	562	0.84	0.89	46	empty
3	748	0.83	0.86	61	FAD
4	724	0.82	0.86	65	FAD, GOL
5	702	0.82	0.86	47	FAD

Interfaces

4 interfaces between chains.

A–B · 1603 Å² buried · 30 hydrogen bonds · protein-protein
C–D · 1599 Å² buried · 29 hydrogen bonds · protein-protein
B–C · 1533 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 1415 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6X24 · Structural basis of plant blue light photoreceptor · the same entry in another collection · chain D against D, TM-score 1.00
Q96524 · AlphaFold monomer V2.0 prediction for cryptochrome-2 (Q96524) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q96524
Elsewhere: RCSB PDB 6X24 · PDBe 6X24 · UniProt Q96524

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