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High-resolution structure of no-nucleotide kinesin on microtubules

Analyse High-resolution structure of no-nucleotide 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: 3J8X
Type: protein
Length: 1,177 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: GTP, GDP
Pockets: 19 · best druggability 0.83

Structure

electron microscopy · 3 distinct chains · 43% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
K	Kinesin-1 heavy chain	protein	316	33% helix, 28% strand	P33176
A	Tubulin alpha-1B chain	protein	430	47% helix, 15% strand	Q2XVP4
B	Tubulin beta-2B chain	protein	431	46% helix, 16% strand	F2Z5B2

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · chains A, B
GDP · Guanosine-5'-diphosphate · ligand · chains B

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

Pockets

19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	509	0.83	0.90	73	GTP
2	1166	0.82	0.83	110	empty
3	427	0.69	0.81	49	empty
4	316	0.60	0.78	40	GDP
5	250	0.56	0.77	37	empty

Interfaces

3 interfaces between chains.

A–B · 1869 Å² buried · 30 hydrogen bonds · protein-protein
K–B · 837 Å² buried · 12 hydrogen bonds · protein-protein
K–A · 813 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3J8X · High-resolution structure of no-nucleotide 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 0.91

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 3J8X · PDBe 3J8X · UniProt P33176 · UniProt Q2XVP4 · UniProt F2Z5B2

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