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KIF2C-darpin fusion protein bound to tubulin

Analyse KIF2C-darpin fusion protein bound to tubulin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MIO
Type: protein
Length: 1,329 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha-1B chain; Tubulin beta chain; Kinesin-like protein KIF2C,KIF2C fused to a…
UniProt: P81947, D0VWY9, Q99661
Ligands: GTP, GDP, LOC, ANP, MG
Pockets: 16 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha-1B chain	protein	429	46% helix, 18% strand	P81947
B	Tubulin beta chain	protein	423	48% helix, 20% strand	D0VWY9
C	Kinesin-like protein KIF2C,KIF2C fused to a DARPIN,KIF2C fused to a darpin	protein	477	39% helix, 21% strand	Q99661

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · chains A, B
GDP · Guanosine-5'-diphosphate · ligand · chains B
LOC · N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide · ligand · chains A, B
ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains C
MG · Magnesium ion · metal · 2 copies · chains A, B, C

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

Pockets

16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	855	0.83	0.86	88	GTP, MG, LOC
2	1133	0.81	0.82	86	empty
3	620	0.68	0.77	78	empty
4	174	0.66	0.86	33	GDP
5	230	0.65	0.83	31	empty

Interfaces

3 interfaces between chains.

B–C · 1366 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1339 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 1052 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5MIO · KIF2C-darpin fusion protein bound to tubulin · the same entry in another collection · chain A against A, TM-score 1.00
Q99661 · AlphaFold monomer V2.0 prediction for kinesin-like protein KIF2C (Q99661) · a predicted model of the same protein · chain C against A, TM-score 0.64

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 P81947
Every structure of UniProt D0VWY9
Every structure of UniProt Q99661
Elsewhere: RCSB PDB 5MIO · PDBe 5MIO · UniProt P81947 · UniProt D0VWY9 · UniProt Q99661

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