MolNFT v1 · #179849 · protein

Cpoga in complex with ligand 54

7KHV · O-glcnacase nagj: “Cpoga in complex with ligand 54”. X-ray diffraction, 4 ligands (X1A, CA, SO4), 20 pockets (best druggability 0.70). MolNFT v1 #179849 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7KHV
Type: protein
Length: 3,466 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: O-glcnacase nagj
EC: 3.2.1.169
UniProt: Q0TR53
Ligands: X1A, CA, SO4, CL
Pockets: 20 · best druggability 0.70

Structure

x-ray diffraction · 3 distinct chains · 48% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	O-glcnacase nagj (EC 3.2.1.169)	protein	586	47% helix, 15% strand	Q0TR53
B, C, D	O-glcnacase nagj (EC 3.2.1.169)	protein	585	47% helix, 15% strand	Q0TR53
F	O-glcnacase nagj (EC 3.2.1.169)	protein	539	50% helix, 12% strand	Q0TR53

Ligands and binding sites

X1A · N-(5-{[6-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)-2,6-diazaspiro[3.4]octan-2-yl]methyl}-1,3-thiazol-2-yl)acetamide · ligand · 6 copies · chains A, B, C, D, E, F
CA · Calcium ion · metal · 3 copies · chains A, D, E
SO4 · Sulfate ion · ion · 35 copies · chains A, B, C, D, E, F
CL · Chloride ion · ion · 5 copies · chains B, C, D, F

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	124	0.70	0.91	25	X1A
2	926	0.70	0.75	87	empty
3	859	0.69	0.75	91	empty
4	116	0.68	0.90	25	X1A
5	111	0.67	0.90	23	X1A

Interfaces

6 interfaces between chains.

C–D · 1085 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 1083 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 1066 Å² buried · 9 hydrogen bonds · protein-protein
D–E · 640 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 444 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

7KHV · CpOGA IN COMPLEX WITH LIGAND 54 · the same entry in another collection · chain F against F, TM-score 1.00
Q0TR53 · AlphaFold monomer V2.0 prediction for O-glcnacase nagj (Q0TR53) · a predicted model of the same protein · chain A 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 Q0TR53
Elsewhere: RCSB PDB 7KHV · PDBe 7KHV · UniProt Q0TR53

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