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Kinesin motor domain in the ADP-mg-alfx state in complex with tubulin and a darpin

Analyse Kinesin motor domain in the ADP-mg-alfx state in complex with tubulin and a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4HNA
Type: protein
Length: 1,353 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha chain; Tubulin beta chain; Designed ankyrin repeat protein (darpin) D2…
UniProt: D0VWZ0, D0VWY9, P33176
Ligands: ALF, GTP, GDP, ADP, MG
Pockets: 13 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 45% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha chain	protein	430	47% helix, 17% strand	D0VWZ0
B	Tubulin beta chain	protein	431	49% helix, 19% strand	D0VWY9
D	Designed ankyrin repeat protein (darpin) D2	protein	159	56% helix, 0% strand	—
K	Kinesin-1 heavy chain	protein	333	33% helix, 29% strand	P33176

Ligands and binding sites

ALF · Tetrafluoroaluminate ion · ligand · 2 copies · chains B, K
GTP · Guanosine-5'-triphosphate · ligand · chains A, B
GDP · Guanosine-5'-diphosphate · ligand · chains B
ADP · Adenosine-5'-diphosphate · ligand · chains K
MG · Magnesium ion · metal · 3 copies · chains A, B, 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	1098	0.80	0.82	109	GTP, MG
2	1147	0.79	0.81	80	empty
3	697	0.69	0.77	56	empty
4	188	0.60	0.82	36	GDP, MG, ALF
5	204	0.59	0.81	31	empty

Interfaces

4 interfaces between chains.

A–B · 1444 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 681 Å² buried · 13 hydrogen bonds · protein-protein
A–K · 660 Å² buried · 6 hydrogen bonds · protein-protein
B–K · 614 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

4HNA · Kinesin motor domain in the ADP-MG-ALFX state in complex with tubulin and a DARPIN · the same entry in another collection · chain A against A, 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 D0VWZ0
Every structure of UniProt D0VWY9
Every structure of UniProt P33176
Elsewhere: RCSB PDB 4HNA · PDBe 4HNA · UniProt D0VWZ0 · UniProt D0VWY9 · UniProt P33176

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