MolNFT v1 · #154502 · protein

Binding pose 1 of 2-CF3 bound asqj complex

6KD9 · IRON/ALPHA-ketoglutarate-dependent dioxygenase asqj: “Binding pose 1 of 2-CF3 bound asqj complex”. X-ray diffraction, 2 ligands (CV3, FE), 5 pockets (best druggability 0.83). MolNFT v1 #154502 on GenesisL1: 3D structure, binding…

PDB: 6KD9
Type: protein
Length: 574 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: IRON/ALPHA-ketoglutarate-dependent dioxygenase asqj
EC: 1.14.-.-
UniProt: Q5AR53
Ligands: CV3, FE
Pockets: 5 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 23% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, F	IRON/ALPHA-ketoglutarate-dependent dioxygenase asqj (EC 1.14.-.-)	protein	287	23% helix, 22% strand	Q5AR53

Ligands and binding sites

CV3 · (3~{Z})-4-methyl-3-[[4-(trifluoromethyl) phenyl]methylidene]-1~{H}-1,4-benzodiazepine-2,5-dione · ligand · 2 copies · chains B, F
FE · Fe (III) ion · metal · 2 copies · chains B, F
SIN · Succinic acid · additive · 2 copies · chains B, F

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

Pockets

5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	177	0.83	0.98	29	empty
2	416	0.83	0.91	55	FE, CV3, SIN
3	399	0.81	0.90	49	FE, CV3, SIN
4	197	0.58	0.81	28	empty
5	186	0.56	0.80	24	empty

Interfaces

1 interface between chains.

B–F · 2918 Å² buried · 49 hydrogen bonds · protein-protein

Compared structures

6KD9 · Binding pose 1 of 2-CF3 bound AsqJ complex · the same entry in another collection · chain B against B, TM-score 1.00
Q5AR53 · AlphaFold monomer V2.0 prediction for IRON/ALPHA-ketoglutarate- dependent dioxygenase… · 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 Q5AR53
Elsewhere: RCSB PDB 6KD9 · PDBe 6KD9 · UniProt Q5AR53

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