Research workbench

Monomeric kinesin-1 motor domain in no-nucleotide state bound to gmpcpp-stabilized microtubule

Analyse Monomeric kinesin-1 motor domain in no-nucleotide state bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6OJQ
Type: protein
Length: 1,164 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin beta-2B chain; Tubulin alpha-1B chain; Kinesin-1 heavy chain
UniProt: Q6B856, P81947, P33176
Ligands: G2P, GTP, MG
Pockets: 15 · best druggability 0.83

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Tubulin beta-2B chain	protein	426	47% helix, 18% strand	Q6B856
A	Tubulin alpha-1B chain	protein	428	47% helix, 14% strand	P81947
K	Kinesin-1 heavy chain	protein	310	33% helix, 27% strand	P33176

Ligands and binding sites

G2P · Phosphomethylphosphonic acid guanylate ester · ligand · chains B
GTP · Guanosine-5'-triphosphate · ligand · chains B, A
MG · Magnesium ion · metal · 2 copies · chains B, A

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

Pockets

15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	248	0.83	0.96	40	GTP, MG
2	1168	0.82	0.83	123	empty
3	319	0.68	0.82	41	G2P, MG
4	337	0.66	0.81	52	empty
5	218	0.54	0.78	26	empty

Interfaces

3 interfaces between chains.

B–A · 2016 Å² buried · 33 hydrogen bonds · protein-protein
A–K · 856 Å² buried · 7 hydrogen bonds · protein-protein
B–K · 655 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6OJQ · Monomeric kinesin-1 motor domain in no-nucleotide state bound to GMPCPP-stabilized… · the same entry in another collection · chain B against B, 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 0.92

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 Q6B856
Every structure of UniProt P81947
Every structure of UniProt P33176
Elsewhere: RCSB PDB 6OJQ · PDBe 6OJQ · UniProt Q6B856 · UniProt P81947 · UniProt P33176

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