5ZO8: Eg5 motor domain

Eg5 motor domain in complex with STLC-type inhibitor PVEI0021 (P21 type). Determined by X-ray diffraction at 2.2 Å resolution. Released 10 Oct 2018.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,467
Mol. weight: 84.72 kDa
Ligands: 4C5, MG, ADP
Released: 10 Oct 2018

Explore 5ZO8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5ZO8 contains 41 α-helices and 43 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 21 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	17-18	2	1
α-helix	19	1
β-strand	20-25	6	2
α-helix	26-28	3
β-strand	41-44	4	3
β-strand	49-53	5	3
β-strand	63-67	5	3
β-strand	70-72	3	2
α-helix	78-81	4
α-helix	82-86	5
α-helix	87-94	8
β-strand	97	1	4
β-strand	98-105	8	2
α-helix	111-115	5
β-strand	117	1	5
α-helix	119-120	2
α-helix	121-123	3
β-strand	133	1	5
α-helix	135-148	14
β-strand	153-164	12	2
β-strand	167-170	4	2
β-strand	182	1	2
β-strand	183-186	4	6
β-strand	194-197	4	6
β-strand	202-204	3	2
α-helix	207-209	3
α-helix	210-227	18
α-helix	231-234	4
β-strand	236-248	13	2
β-strand	254-265	12	2
α-helix	266-268	3
α-helix	290-303	14
α-helix	311-313	3
α-helix	315-319	5
α-helix	321-323	3
β-strand	328-336	9	2
α-helix	340-342	3
α-helix	343-355	13
α-helix	356-358	3
α-helix	359	1
β-strand	360-361	2	1
β-strand	365	1	4
β-strand	366	1	2

Chain B: 20 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	17-18	2	7
α-helix	19	1
β-strand	20-25	6	8
α-helix	26-28	3
β-strand	41-44	4	9
β-strand	49-53	5	9
β-strand	63-67	5	9
β-strand	70-72	3	8
α-helix	78-81	4
α-helix	82-86	5
α-helix	87-94	8
β-strand	97	1	10
β-strand	98-105	8	8
α-helix	111-115	5
β-strand	117	1	11
α-helix	119-120	2
α-helix	121-123	3
β-strand	133	1	11
α-helix	135-148	14
β-strand	153-164	12	8
β-strand	167-170	4	8
β-strand	182	1	8
β-strand	183-187	5	12
β-strand	190-197	8	12
β-strand	202-204	3	8
α-helix	207-209	3
α-helix	210-227	18
α-helix	231-234	4
β-strand	236-248	13	8
β-strand	254-265	12	8
α-helix	266-268	3
α-helix	290-303	14
α-helix	311-313	3
α-helix	315-319	5
α-helix	321-323	3
β-strand	329-336	8	8
α-helix	340-342	3
α-helix	343-356	14
α-helix	359	1
β-strand	360-361	2	7
β-strand	365	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kinesin-like protein KIF11	A, B	protein	367	Homo sapiens	P52732 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5ZO8_1 Kinesin-like protein KIF11 (chains A, B)
MNHKVHMKNIQVVVRCRPFNLAERKASAHSIVECDPVRKEVSVRTGGLADKSSRKTYTFD
MVFGASTKQIDVYRSVVCPILDEVIMGYNCTIFAYGQTGTGKTFTMEGERSPNEEYTWEE
DPLAGIIPRTLHQIFEKLTDNGTEFSVKVSLLEIYNEELFDLLNPSSDVSERLQMFDDPR
NKRGVIIKGLEEITVHNKDEVYQILEKGAAKRTTAATLMNAYSSRSHSVFSVTIHMKETT
IDGEELVKIGKLNLVDLAGSENIGRSGAVDKRAREAGNINQSLLTLGRVITALVERTPHV
PYRESKLTRILQDSLGGRTRTSIIATISPASLNLEETLSTLEYAHRAKNILNKPEVNQKL
QHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
4C5	(2R)-2-azanyl-3-[(4-methoxyphenyl)-diphenyl-methyl]sulfanyl-propanoic acid	C23 H23 N O3 S	2
MG	Magnesium ion	Mg	2
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2

Water and common crystallization additives (NA, SO4) are not listed.

Primary citation

Structural and Thermodynamic Basis of the Enhanced Interaction between Kinesin Spindle Protein Eg5 and STLC-type Inhibitors. Yokoyama, H., Sawada, J.I., Sato, K. et al. ACS Omega (2018) 3:12284-12294. DOI 10.1021/acsomega.8b00778 · PubMed

Other PDB entries of the same protein (UniProt P52732 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3ZCW 1.69 Å, Eg5 - New allosteric binding site
6TLE 1.75 Å, Human Eg5 motor domain mutant E344K
1X88 1.8 Å, Human Eg5 motor domain bound to Mg-ADP and monastrol
6G6Y 1.8 Å, Eg5-inhibitor complex
2PG2 1.85 Å, Crystal structure of KSP in complex with ADP and thiophene containing inhibitor 15
1Q0B 1.9 Å, Crystal structure of the motor protein KSP in complex with ADP and monastrol
2X7C 1.9 Å, Crystal structure of human kinesin Eg5 in complex with (S)-enastron
8YHH 1.95 Å, The Crystal Structure of Mitotic Kinesin Eg5 from Biortus
3K5E 1.97 Å, The structure of human kinesin-like motor protein Kif11/KSP/Eg5 in complex with ADP and…
2WOG 2.0 Å, Intermediate and final states of human kinesin Eg5 in complex with S-trityl-L-cysteine
3L9H 2.0 Å, X-ray structure of mitotic kinesin-5 (KSP, KIF11, Eg5)in complex with the…
5JV3 2.01 Å, The neck-linker and alpha 7 helix of Homo sapiens Eg5 fused to EB1

Browse structure collections

About this viewer

MolViewer shows 5ZO8 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.