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Crystal structure of drosophila melanogaster kinesin-1 motor domain dimer-tail complex

Analyse Crystal structure of drosophila melanogaster kinesin-1 motor domain dimer-tail… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2Y65
Type: protein
Length: 1,388 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kinesin heavy chain
UniProt: P17210
Ligands: ADP, MG
Pockets: 14 · best druggability 0.79

Structure

x-ray diffraction · 6 distinct chains · 34% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Kinesin heavy chain	protein	328	34% helix, 29% strand	P17210
B	Kinesin heavy chain	protein	341	34% helix, 29% strand	P17210
C	Kinesin heavy chain	protein	343	35% helix, 29% strand	P17210
D	Kinesin heavy chain	protein	338	35% helix, 27% strand	P17210
W, X	Kinesin heavy chain	protein	13	0% helix, 31% strand	P17210
Y	Kinesin heavy chain	protein	12	0% helix, 17% strand	P17210

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

14 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	1019	0.79	0.81	112	empty
2	821	0.77	0.81	110	ADP, MG
3	251	0.58	0.79	40	empty
4	335	0.54	0.74	43	empty
5	159	0.52	0.79	28	MG

Interfaces

10 interfaces between chains.

C–D · 834 Å² buried · 7 hydrogen bonds · protein-protein
C–W · 628 Å² buried · 12 hydrogen bonds · protein-protein
B–X · 626 Å² buried · 10 hydrogen bonds · protein-protein
A–Y · 623 Å² buried · 7 hydrogen bonds · protein-protein
D–W · 551 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

2Y65 · Crystal structure of Drosophila melanogaster kinesin-1 motor domain dimer-tail complex · the same entry in another collection · chain Y against Y, TM-score 1.00
P17210 · AlphaFold monomer V2.0 prediction for kinesin heavy chain (P17210) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P17210
Elsewhere: RCSB PDB 2Y65 · PDBe 2Y65 · UniProt P17210

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