MolNFT v1 · #90781 · protein

Kinesin-like protein KAR3 and Spindle pole body-associated protein VIK1

4ETP · Kinesin-like protein KAR3 and Spindle pole body-associated protein VIK1. X-ray diffraction, 3 ligands (ADP, EBC, MG), 9 pockets (best druggability 0.60). MolNFT v1 #90781 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4ETP
Type: protein
Length: 666 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kinesin-like protein KAR3; Spindle pole body-associated protein VIK1
UniProt: P17119, Q12045
Ligands: ADP, EBC, MG
Pockets: 9 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Kinesin-like protein KAR3	protein	379	43% helix, 24% strand	P17119
B	Spindle pole body-associated protein VIK1	protein	287	43% helix, 24% strand	Q12045

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
EBC · N,N'-ethane-1,2-diylbis(2-iodoacetamide) · ligand · chains B
MG · Magnesium ion · metal · chains A
GOL · Glycerol · additive · 6 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	376	0.60	0.76	34	empty
2	132	0.53	0.81	16	empty
3	128	0.51	0.80	31	GOL
4	76	0.44	0.81	17	empty
5	126	0.43	0.77	22	empty

Interfaces

1 interface between chains.

A–B · 1608 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

4ETP · C-terminal motor and motor homology domain of Kar3Vik1 fused to a synthetic heterodimeric… · the same entry in another collection · chain A against A, TM-score 1.00
Q12045 · AlphaFold monomer V2.0 prediction for spindle pole body-associated protein VIK1 (Q12045) · a predicted model of the same protein · chain B against A, TM-score 0.98
P17119 · AlphaFold monomer V2.0 prediction for kinesin-like protein KAR3 (P17119) · 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 P17119
Every structure of UniProt Q12045
Elsewhere: RCSB PDB 4ETP · PDBe 4ETP · UniProt P17119 · UniProt Q12045

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