5W3D: Kinesin-14 wild-type Ncd-ADP dimer

Name: PDB 5W3D: The structure of kinesin-14 wild-type Ncd-ADP dimer
Published: 2017-12-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: motor protein

The structure of kinesin-14 wild-type Ncd-ADP dimer. Determined by X-ray diffraction at 2.79 Å resolution. Released 20 Dec 2017.

Method: X-ray diffraction
Resolution: 2.79 Å
Organism: Drosophila melanogaster
Chains: 2
Atoms: 5,346
Mol. weight: 94.42 kDa
Ligands: ADP, MG
Released: 20 Dec 2017

Explore 5W3D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W3D contains 31 α-helices and 37 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: 17 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	293-346	54
β-strand	349-355	7	1
α-helix	356-359	4
α-helix	366	1
β-strand	367	1	2
β-strand	369-371	3	3
β-strand	377-381	5	3
β-strand	394-397	4	3
β-strand	400-402	3	1
α-helix	408-413	6
α-helix	416-423	8
β-strand	428-433	6	1
α-helix	440-444	5
β-strand	446-447	2	4
β-strand	450-451	2	4
α-helix	453-468	16
α-helix	469-471	3
β-strand	473-485	13	1
β-strand	488-491	4	1
β-strand	502-504	3	5
β-strand	512-514	3	5
β-strand	520-521	2	1
α-helix	525-538	14
α-helix	550-552	3
β-strand	554-565	12	1
β-strand	570-580	11	1
α-helix	581-583	3
α-helix	602-614	13
α-helix	622-624	3
α-helix	626-630	5
α-helix	632-634	3
β-strand	640-647	8	1
β-strand	650	1	2
α-helix	651-653	3
α-helix	654-669	16

Chain B: 14 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	295-345	51
β-strand	349-355	7	6
α-helix	356-359	4
α-helix	366	1
β-strand	367	1	7
α-helix	368	1
β-strand	369-372	4	8
β-strand	377-381	5	8
β-strand	395-397	3	8
β-strand	400-402	3	6
α-helix	408-413	6
α-helix	416-424	9
β-strand	427-434	8	6
α-helix	440-444	5
β-strand	446-447	2	9
β-strand	450-451	2	9
α-helix	453-468	16
β-strand	474-479	6	10
β-strand	482-484	3	6
β-strand	489-491	3	6
β-strand	520-522	3	10
α-helix	525-538	14
β-strand	554-556	3	6
β-strand	558	1	6
β-strand	561-564	4	10
β-strand	575-580	6	6
α-helix	581-583	3
α-helix	601-614	14
α-helix	627-630	4
β-strand	641-647	7	6
β-strand	650	1	7
α-helix	651-653	3
α-helix	654-667	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein claret segregational	A, B	protein	412	Drosophila melanogaster	P20480 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5W3D_1 Protein claret segregational (chains A, B)
MGSMHAALSTEVVHLRQRTEELLRCNEQQAAELETCKEQLFQSNMERKELHNTVMDLRGN
IRVFCRIRPPLESEENRMCCTWTYHDESTVELQSIDAQAKSKMGQQIFSFDQVFHPLSSQ
SDIFEMVSPLIQSALDGYNICIFAYGQTGSGKTYTMDGVPESVGVIPRTVDLLFDSIRGY
RNLGWEYEIKATFLEIYNEVLYDLLSNEQKDMEIRMAKNNKNDIYVSNITEETVLDPNHL
RHLMHTAKMNRATASTAGNERSSRSHAVTKLELIGRHAEKQEISVGSINLVDLAGSESPK
TSTRMTETKNINRSLSELTNVILALLQKQDHIPYRNSKLTHLLMPSLGGNSKTLMFINVS
PFQDCFQESVKSLRFAASVNSCKMTKAKRNRYLNNSVANSSTQSNNSGNFDK

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
MG	Magnesium ion	Mg	2

Primary citation

Structural basis of small molecule ATPase inhibition of a human mitotic kinesin motor protein. Park, H.W., Ma, Z., Zhu, H. et al. Sci Rep (2017) 7:15121-15121. DOI 10.1038/s41598-017-14754-6 · PubMed

Other PDB entries of the same protein (UniProt P20480 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3U06 2.35 Å, Crystal structure of the kinesin-14 NcdG347D
1N6M 2.5 Å, Rotation of the stalk/neck and one head in a new crystal structure of the kinesin motor…
2NCD 2.5 Å, Ncd (non-claret disjunctional) dimer from D. Melanogaster
3L1C 2.75 Å, Kinesin-14 Protein Ncd, T436S Mutant
1CZ7 2.9 Å, The crystal structure of a minus-end directed microtubule motor protein ncd reveals…
5HLE 2.9 Å, Structural basis of backwards motion in kinesin-14: minus-end directed nKn664 in the ADP…
8YUE 3.15 Å, Crystal structure of the kinesin-14 motor protein from Drosophila melanogaster
8YY3 3.24 Å, Kinesin-14 in nucleotide-free state bound to 14 PF Microtubule
8YY2 3.6 Å, Kinesin-14 in nucleotide-free state bound to 13 PF Microtubule
8YY5 3.99 Å, Kinesin-14 with AlF3 bound to 14 PF Microtubule
8YY4 4.02 Å, Kinesin-14 with AlF3 bound to 13 PF Microtubule
5HNZ 5.8 Å, Structural basis of backwards motion in kinesin-14: plus-end directed nKn669 in the…

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