Research workbench

BON1

Analyse BON1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6KXU
Type: protein
Length: 4,290 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein bonzai 1
UniProt: Q941L3
Ligands: MN, CL
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 6 distinct chains · 24% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein bonzai 1	protein	546	24% helix, 34% strand	Q941L3
B	Protein bonzai 1	protein	504	23% helix, 35% strand	Q941L3
C, D, F	Protein bonzai 1	protein	553	24% helix, 33% strand	Q941L3
E	Protein bonzai 1	protein	534	24% helix, 33% strand	Q941L3
G	Protein bonzai 1	protein	504	23% helix, 35% strand	Q941L3
H	Protein bonzai 1	protein	543	24% helix, 33% strand	Q941L3

Ligands and binding sites

MN · Manganese (II) ion · metal · 10 copies · chains A, B, C, D, E, F, G, H
CL · Chloride ion · ion · 2 copies · chains C, D
EDO · 1,2-ethanediol · additive · 14 copies · chains A, B, C, E, D, F, G, H
GOL · Glycerol · additive · chains A

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	1114	0.77	0.79	88	empty
2	976	0.77	0.79	99	EDO
3	651	0.75	0.81	50	EDO
4	314	0.73	0.85	43	empty
5	514	0.70	0.80	53	EDO

Interfaces

12 interfaces between chains.

D–G · 1098 Å² buried · 13 hydrogen bonds · protein-protein
B–F · 1035 Å² buried · 15 hydrogen bonds · protein-protein
B–D · 588 Å² buried · 4 hydrogen bonds · protein-protein
C–E · 544 Å² buried · 5 hydrogen bonds · protein-protein
E–F · 515 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6KXU · BON1 · the same entry in another collection · chain H against H, TM-score 1.00
Q941L3 · AlphaFold monomer V2.0 prediction for protein bonzai 1 (Q941L3) · a predicted model of the same protein · chain G 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 Q941L3
Elsewhere: RCSB PDB 6KXU · PDBe 6KXU · UniProt Q941L3

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