MolNFT v1 · #27054 · protein

Human EG5 motor domain bound to mg-ADP and monastrol

1X88 · Kinesin-like protein KIF11: “Human EG5 motor domain bound to mg-ADP and monastrol”. X-ray diffraction, 3 ligands (ADP, NAT, MG), 9 pockets (best druggability 0.66). MolNFT v1 #27054 on GenesisL1: 3D structure, binding sites and…

PDB: 1X88
Type: protein
Length: 666 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kinesin-like protein KIF11
UniProt: P52732
Ligands: ADP, NAT, MG
Pockets: 9 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Kinesin-like protein KIF11	protein	332	34% helix, 32% strand	P52732
B	Kinesin-like protein KIF11	protein	334	34% helix, 29% strand	P52732

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
NAT · Ethyl 4-(3-hydroxyphenyl)-6-methyl-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

9 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	327	0.66	0.81	56	MG, ADP, NAT
2	584	0.62	0.74	48	empty
3	356	0.61	0.78	32	empty
4	299	0.59	0.78	28	empty
5	138	0.56	0.82	24	NAT

Interfaces

1 interface between chains.

A–B · 282 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

1X88 · Human Eg5 motor domain bound to Mg-ADP and monastrol · the same entry in another collection · chain A against A, TM-score 1.00
P52732 · AlphaFold monomer V2.0 prediction for kinesin-like protein KIF11 (P52732) · a predicted model of the same protein · chain A 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 P52732
Elsewhere: RCSB PDB 1X88 · PDBe 1X88 · UniProt P52732

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