Research workbench

High-resolution structure of ATP analog-bound kinesin on microtubules

Analyse High-resolution structure of ATP analog-bound kinesin on microtubules in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3J8Y
Type: protein
Length: 1,191 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kinesin-1 heavy chain; Tubulin alpha-1B chain; Tubulin beta-2B chain
UniProt: P33176, Q2XVP4, F2Z5B2
Ligands: ATP, GTP, GDP, MG
Pockets: 13 · best druggability 0.82

Structure

electron microscopy · 3 distinct chains · 42% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
K	Kinesin-1 heavy chain	protein	330	35% helix, 30% strand	P33176
A	Tubulin alpha-1B chain	protein	430	43% helix, 18% strand	Q2XVP4
B	Tubulin beta-2B chain	protein	431	46% helix, 19% strand	F2Z5B2

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · chains K
GTP · Guanosine-5'-triphosphate · ligand · chains A, B
GDP · Guanosine-5'-diphosphate · ligand · chains B
MG · Magnesium ion · metal · chains K

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

Pockets

13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	761	0.82	0.85	100	GTP
2	819	0.80	0.83	63	empty
3	249	0.64	0.82	39	GDP
4	334	0.63	0.79	49	empty
5	264	0.56	0.77	42	empty

Interfaces

3 interfaces between chains.

A–B · 1843 Å² buried · 26 hydrogen bonds · protein-protein
K–A · 749 Å² buried · 6 hydrogen bonds · protein-protein
K–B · 727 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

3J8Y · High-resolution structure of ATP analog-bound kinesin on microtubules · the same entry in another collection · chain K against K, TM-score 1.00
P33176 · AlphaFold monomer V2.0 prediction for kinesin-1 heavy chain (P33176) · a predicted model of the same protein · chain K against A, TM-score 0.95

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 P33176
Every structure of UniProt Q2XVP4
Every structure of UniProt F2Z5B2
Elsewhere: RCSB PDB 3J8Y · PDBe 3J8Y · UniProt P33176 · UniProt Q2XVP4 · UniProt F2Z5B2

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