MolNFT v1 · #40806 · protein

Cryptochrome 3 from arabidopsis thaliana

2J4D · Cryptochrome dash: “Cryptochrome 3 from arabidopsis thaliana”. X-ray diffraction, 2 ligands (FAD, MHF), 12 pockets (best druggability 0.83). MolNFT v1 #40806 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2J4D
Type: protein
Length: 995 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cryptochrome dash
UniProt: Q84KJ5
Ligands: FAD, MHF
Pockets: 12 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cryptochrome dash	protein	496	48% helix, 8% strand	Q84KJ5
B	Cryptochrome dash	protein	499	48% helix, 8% strand	Q84KJ5

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
MHF · 5,10-methenyl-6,7,8-trihydrofolic acid · ligand · 2 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, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	548	0.83	0.89	44	FAD
2	542	0.83	0.89	43	FAD
3	447	0.82	0.90	67	MHF
4	420	0.81	0.89	53	MHF
5	1136	0.76	0.78	63	empty

Interfaces

1 interface between chains.

A–B · 885 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

2J4D · Cryptochrome 3 from Arabidopsis thaliana · the same entry in another collection · chain B against B, TM-score 1.00
Q84KJ5 · AlphaFold monomer V2.0 prediction for cryptochrome dash, CHLOROPLASTIC/MITOCHONDRIAL… · a predicted model of the same protein · chain B 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 Q84KJ5
Elsewhere: RCSB PDB 2J4D · PDBe 2J4D · UniProt Q84KJ5

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