Structure of PDB 5yl2 Chain A

Receptor sequence

>5yl2A (length=437) Species: 9823 (Sus scrofa)

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFN
TFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAA
NNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFT
SLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDC
AFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNV
DLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTG
FKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYA
KRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGV

3D structure

• PDB: 5yl2 The compound millepachine and its derivatives inhibit tubulin polymerization by irreversibly binding to the colchicine-binding site in beta-tubulin.
• Chain: A
• Resolution: 2.09 Å

Enzymatic activity

• Enzyme Commision number: 3.6.5.-

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	GTP	A	G10 Q11 A12 Q15 A99 N101 S140 G143 G144 T145 G146 V177 T179 E183 N206 Y224 N228	G10 Q11 A12 Q15 A99 N101 S140 G143 G144 T145 G146 V177 T179 E183 N206 Y224 N228
BS02	CA	A	D39 T41 G44 E55	D39 T41 G44 E55
BS03	8WU	A	T179 A180 V181	T179 A180 V181	PDBbind-CN: -logKd/Ki=4.50,Kd=31.69uM

Gene Ontology

Molecular Function

• GO:0003924 GTPase activity
• GO:0005200 structural constituent of cytoskeleton
• GO:0005525 GTP binding
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0000226 microtubule cytoskeleton organization
• GO:0000278 mitotic cell cycle
• GO:0007017 microtubule-based process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005856 cytoskeleton
• GO:0005874 microtubule
• GO:0015630 microtubule cytoskeleton

External links

• PDB: RCSB:5yl2, PDBe:5yl2, PDBj:5yl2
• PDBsum: 5yl2
• PubMed: 29691282
• UniProt: Q2XVP4|TBA1B_PIG Tubulin alpha-1B chain (Gene Name=TUBA1B)