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Molecular basis of human kinesin-8 function and inhibition

Analyse Molecular basis of human kinesin-8 function and inhibition in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5OGC
Type: protein
Length: 1,166 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kinesin-like protein KIF18A; Tubulin alpha chain; Tubulin beta chain
UniProt: Q8NI77, F2Z4C1, P02554
Ligands: 9V5, GTP, GDP, TA1, ZN, MG
Pockets: 18 · best druggability 0.83

Structure

electron microscopy · 3 distinct chains · 43% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
K	Kinesin-like protein KIF18A	protein	328	38% helix, 23% strand	Q8NI77
A	Tubulin alpha chain	protein	412	43% helix, 14% strand	F2Z4C1
B	Tubulin beta chain	protein	426	45% helix, 17% strand	P02554

Ligands and binding sites

9V5 · 4-chloranyl-2-nitro-1-(phenylsulfonyl)benzene · ligand · chains K
GTP · Guanosine-5'-triphosphate · ligand · chains A, B
GDP · Guanosine-5'-diphosphate · ligand · chains B
TA1 · Taxol · ligand · chains B
ZN · Zinc ion · metal · chains A
MG · Magnesium ion · metal · chains A

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

Pockets

18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	212	0.83	0.96	40	MG, GTP
2	1050	0.80	0.81	85	empty
3	494	0.78	0.86	74	empty
4	176	0.68	0.87	35	9V5
5	52	0.68	0.96	24	empty

Interfaces

3 interfaces between chains.

A–B · 1840 Å² buried · 25 hydrogen bonds · protein-protein
K–A · 753 Å² buried · 9 hydrogen bonds · protein-protein
K–B · 596 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5OGC · Molecular basis of human kinesin-8 function and inhibition · the same entry in another collection · chain K against K, TM-score 1.00
Q8NI77 · AlphaFold monomer V2.0 prediction for kinesin-like protein KIF18A (Q8NI77) · a predicted model of the same protein · chain K against A, TM-score 0.89

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 Q8NI77
Every structure of UniProt F2Z4C1
Every structure of UniProt P02554
Elsewhere: RCSB PDB 5OGC · PDBe 5OGC · UniProt Q8NI77 · UniProt F2Z4C1 · UniProt P02554

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