MolNFT v1 · #107475 · protein

Hsmcak motor domain complex

4UBF · Kinesin-like protein KIF2C: “Hsmcak motor domain complex”. X-ray diffraction, 2 ligands (ADP, MG), 20 pockets (best druggability 0.71). MolNFT v1 #107475 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4UBF
Type: protein
Length: 1,279 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kinesin-like protein KIF2C
UniProt: Q99661
Ligands: ADP, MG
Pockets: 20 · best druggability 0.71

Structure

x-ray diffraction · 5 distinct chains · 28% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Kinesin-like protein KIF2C	protein	309	28% helix, 26% strand	Q99661
B	Kinesin-like protein KIF2C	protein	319	30% helix, 25% strand	Q99661
C	Kinesin-like protein KIF2C	protein	322	29% helix, 24% strand	Q99661
D	Kinesin-like protein KIF2C	protein	322	25% helix, 21% strand	Q99661
P	Kinesin-like protein KIF2C	protein	7	0% helix, 0% strand	Q99661

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 7 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	685	0.71	0.78	62	empty
2	342	0.62	0.78	30	empty
3	369	0.60	0.77	43	empty
4	311	0.60	0.78	34	empty
5	233	0.59	0.80	29	empty

Interfaces

7 interfaces between chains.

A–B · 915 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 868 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 469 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 406 Å² buried · 1 hydrogen bond · protein-protein
A–P · 291 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4UBF · HsMCAK motor domain complex · the same entry in another collection · chain P against P, TM-score 1.00
Q99661 · AlphaFold monomer V2.0 prediction for kinesin-like protein KIF2C (Q99661) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q99661
Elsewhere: RCSB PDB 4UBF · PDBe 4UBF · UniProt Q99661

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