MolNFT v1 · #129108 · protein

Molecular basis of human kinesin-8 function and inhibition

5OAM · Kinesin-like protein KIF18A: “Molecular basis of human kinesin-8 function and inhibition”. Electron microscopy, 5 ligands (GTP, GDP, TA1), 12 pockets (best druggability 0.77). MolNFT v1 #129108 on GenesisL1: 3D structure, binding…

PDB: 5OAM
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: GTP, GDP, TA1, ZN, MG
Pockets: 12 · best druggability 0.77

Structure

electron microscopy · 3 distinct chains · 42% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
K	Kinesin-like protein KIF18A	protein	328	37% helix, 20% strand	Q8NI77
A	Tubulin alpha chain	protein	412	43% helix, 15% strand	F2Z4C1
B	Tubulin beta chain	protein	426	44% helix, 16% strand	P02554

Ligands and binding sites

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

12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1052	0.77	0.80	161	empty
2	874	0.74	0.79	131	empty
3	836	0.74	0.79	151	empty
4	788	0.73	0.79	129	empty
5	663	0.59	0.73	90	empty

Interfaces

2 interfaces between chains.

A–B · 278 Å² buried · 2 hydrogen bonds · protein-protein
K–A · 97 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5OAM · Molecular basis of human kinesin-8 function and inhibition · the same entry in another collection · chain B against B, 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 0.88

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 5OAM · PDBe 5OAM · UniProt Q8NI77 · UniProt F2Z4C1 · UniProt P02554

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