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Crystal structure of human kinesin EG5 in complex with (R)-2-amino-3-((S)-2-methyl-1,1-DIPHENYLBUTYLTHIO)PROPANOIC acid

Analyse Crystal structure of human kinesin EG5 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2XAE
Type: protein
Length: 985 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kinesin-like protein KIF11
UniProt: P52732
Ligands: 2XA, ADP, MG, SO4, CL
Pockets: 15 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Kinesin-like protein KIF11	protein	328	35% helix, 28% strand	P52732
C	Kinesin-like protein KIF11	protein	329	32% helix, 29% strand	P52732

Ligands and binding sites

2XA · (2R)-2-amino-3-[(4-chlorophenyl)-diphenyl-methyl]sulfanyl-propanoic acid · ligand · 3 copies · chains A, B, C
ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
MG · Magnesium ion · metal · 3 copies · chains A, B, C
SO4 · Sulfate ion · ion · 3 copies · chains B, C
CL · Chloride ion · ion · chains 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, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	358	0.63	0.78	36	empty
2	300	0.63	0.80	34	empty
3	169	0.62	0.84	27	2XA
4	167	0.60	0.83	27	2XA
5	148	0.60	0.84	22	2XA

Interfaces

3 interfaces between chains.

A–B · 696 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 685 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 660 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

2XAE · Crystal structure of human kinesin Eg5 in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
P52732 · AlphaFold monomer V2.0 prediction for kinesin-like protein KIF11 (P52732) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P52732
Elsewhere: RCSB PDB 2XAE · PDBe 2XAE · UniProt P52732

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