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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: 6KXK
Type: protein
Length: 4,345 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein bonzai 1
UniProt: Q941L3
Ligands: CA, CL
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 5 distinct chains · 24% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, F	Protein bonzai 1	protein	553	25% helix, 33% strand	Q941L3
B	Protein bonzai 1	protein	528	23% helix, 34% strand	Q941L3
E	Protein bonzai 1	protein	547	25% helix, 33% strand	Q941L3
G	Protein bonzai 1	protein	508	23% helix, 36% strand	Q941L3
H	Protein bonzai 1	protein	550	25% helix, 33% strand	Q941L3

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains D, F
CL · Chloride ion · ion · 2 copies · chains C, D
EDO · 1,2-ethanediol · additive · 81 copies · chains A, B, C, E, D, H, G, F
GOL · Glycerol · additive · 27 copies · chains A, B, F, C, E, D, G, H
PEG · Di(hydroxyethyl)ether · additive · 17 copies · chains A, B, F, C, D, G, E
PGE · Triethylene glycol · additive · 5 copies · chains A, B, C, F
PG4 · Tetraethylene glycol · additive · 2 copies · chains B, 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1028	0.80	0.81	87	EDO
2	951	0.77	0.79	93	GOL, EDO
3	778	0.75	0.80	69	EDO
4	501	0.73	0.82	60	EDO
5	662	0.73	0.79	78	GOL

Interfaces

12 interfaces between chains.

D–G · 1138 Å² buried · 11 hydrogen bonds · protein-protein
B–F · 1031 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 596 Å² buried · 3 hydrogen bonds · protein-protein
C–E · 571 Å² buried · 6 hydrogen bonds · protein-protein
E–F · 496 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6KXK · 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 0.99

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 6KXK · PDBe 6KXK · UniProt Q941L3

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