MolNFT v1 · #156535 · protein

Cryo-EM structure of arabidopsis cry under blue light-mediated activation

6M79 · Cryptochrome-2: “Cryo-EM structure of arabidopsis cry under blue light-mediated activation”. Electron microscopy, 2 ligands (AMP, FAD), 20 pockets (best druggability 0.85). MolNFT v1 #156535 on GenesisL1: 3D structure, binding sites…

PDB: 6M79
Type: protein
Length: 1,842 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cryptochrome-2
UniProt: Q96524
Ligands: AMP, FAD
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 2 distinct chains · 53% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Cryptochrome-2	protein	460	53% helix, 7% strand	Q96524
B, D	Cryptochrome-2	protein	461	53% helix, 7% strand	Q96524

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
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, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1153	0.85	0.86	100	empty
2	1013	0.84	0.84	84	empty
3	1031	0.83	0.83	68	AMP, FAD
4	229	0.82	0.95	35	empty
5	229	0.82	0.95	33	empty

Interfaces

4 interfaces between chains.

A–C · 1455 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 1422 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 1417 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 1406 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

6M79 · Cryo-EM structure of Arabidopsis CRY under blue light-mediated activation · 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 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 Q96524
Elsewhere: RCSB PDB 6M79 · PDBe 6M79 · UniProt Q96524

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.