MolNFT v1 · #164810 · protein

Human kinesin-5 motor domain in the gsk-1 state bound to microtubules (conformation 1)

6TA3 · Tubulin beta chain: “Human kinesin-5 motor domain in the gsk-1 state bound to microtubules (conformation 1)”. Electron microscopy, 3 ligands (G2P, MZK, MG), 20 pockets (best druggability 0.88). MolNFT v1 #164810 on GenesisL1: 3D…

PDB: 6TA3
Type: protein
Length: 1,201 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin beta chain; Tubulin alpha-1B chain; Kinesin-like protein KIF11
UniProt: P02554, Q2XVP4, P52732
Ligands: G2P, MZK, MG
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 3 distinct chains · 46% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Tubulin beta chain	protein	429	51% helix, 11% strand	P02554
A	Tubulin alpha-1B chain	protein	438	49% helix, 10% strand	Q2XVP4
K	Kinesin-like protein KIF11	protein	334	36% helix, 28% strand	P52732

Ligands and binding sites

G2P · Phosphomethylphosphonic acid guanylate ester · ligand · 2 copies · chains B, A
MZK · 6-[4-(trifluoromethyl)phenyl]-3,4-dihydro-1~{H}-quinolin-2-one · ligand · chains A, K
MG · Magnesium ion · metal · 2 copies · chains B, A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	773	0.88	0.92	115	G2P
2	590	0.88	0.93	86	empty
3	261	0.84	0.95	42	empty
4	343	0.82	0.91	72	MZK
5	154	0.77	0.94	33	empty

Interfaces

3 interfaces between chains.

B–A · 1247 Å² buried · 35 hydrogen bonds · protein-protein
A–K · 735 Å² buried · 6 hydrogen bonds · protein-protein
B–K · 494 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 1 isopeptide (covalent ligand, isopeptide).

Compared structures

6TA3 · Human kinesin-5 motor domain in the GSK-1 state bound to microtubules (Conformation 1) · the same entry in another collection · chain B against B, TM-score 1.00

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 P02554
Every structure of UniProt Q2XVP4
Every structure of UniProt P52732
Elsewhere: RCSB PDB 6TA3 · PDBe 6TA3 · UniProt P02554 · UniProt Q2XVP4 · UniProt P52732

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