1W9K: Myosin II heavy chain

Name: PDB 1W9K: Dictyostelium discoideum Myosin II motor domain S456E with bound MgADP-BeFx
Published: 2006-03-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: myosin

Dictyostelium discoideum Myosin II motor domain S456E with bound MgADP-BeFx. Determined by X-ray diffraction at 2.05 Å resolution. Released 16 Mar 2006.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: DICTYOSTELIUM DISCOIDEUM
Chains: 1
Atoms: 6,109
Mol. weight: 88.8 kDa
Ligands: MG, ADP, BEF
Released: 16 Mar 2006

Explore 1W9K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1W9K contains 36 α-helices and 27 β-strands across 1 chain. 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: 36 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	10-15	6
β-strand	34-37	4	1
β-strand	48-55	8	1
β-strand	59-63	5	1
β-strand	69-73	5	1
α-helix	74-76	3
β-strand	78-79	2	1
α-helix	80-82	3
α-helix	83-85	3
β-strand	90	1	2
α-helix	91-93	3
α-helix	99-111	13
β-strand	116-119	4	2
β-strand	122-126	5	2
α-helix	137-143	7
α-helix	148-150	3
α-helix	155-169	15
β-strand	173-178	6	2
α-helix	185-200	16
α-helix	210-226	17
β-strand	227-228	2	3
β-strand	236-237	2	3
β-strand	240-247	8	2
β-strand	253-261	9	2
α-helix	265-268	4
β-strand	278	1	3
α-helix	279-287	9
α-helix	290-295	6
α-helix	301-303	3
α-helix	320-334	15
α-helix	338-355	18
β-strand	360-361	2	4
β-strand	367-368	2	4
α-helix	373-382	10
α-helix	386-394	9
β-strand	397-400	4	5
β-strand	403-406	4	5
α-helix	411-441	31
β-strand	448-454	7	2
β-strand	464	1	6
α-helix	466-497	32
α-helix	506-510	5
α-helix	511-518	8
α-helix	525-533	9
α-helix	540-551	12
β-strand	558-559	2	6
β-strand	567-572	6	6
β-strand	575-580	6	6
α-helix	584-589	6
α-helix	594-601	8
α-helix	606-613	8
α-helix	615-618	4
α-helix	630-646	17
β-strand	649-656	8	2
α-helix	669-678	10
α-helix	681-687	7
β-strand	694-697	4	7
α-helix	698-702	5
α-helix	719-728	10
α-helix	734-736	3
β-strand	737-739	3	7
β-strand	743-746	4	7
α-helix	750-753	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Myosin II heavy chain	A	protein	770	DICTYOSTELIUM DISCOIDEUM	P08799 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1W9K_1 MYOSIN II HEAVY CHAIN (chains A)
MDPIHDRTSDYHKYLKVKQGDSDLFKLTVSDKRYIWYNPDPKERDSYECGEIVSETSDSF
TFKTVDGQDRQVKKDDANQRNPIKFDGVEDMSELSYLNEPAVFHNLRVRYNQDLIYTYSG
LFLVAVNPFKRIPIYTQEMVDIFKGRRRNEVAPHIFAISDVAYRSMLDDRQNQSLLITGE
SGAGKTENTKKVIQYLASVAGRNQANGSGVLEQQILQANPILEAFGNAKTTRNNNSSRFG
KFIEIQFNSAGFISGASIQSYLLEKSRVVFQSETERNYHIFYQLLAGATAEEKKALHLAG
PESFNYLNQSGCVDIKGVSDSEEFKITRQAMDIVGFSQEEQMSIFKIIAGILHLGNIKFE
KGAGEGAVLKDKTALNAASTVFGVNPSVLEKALMEPRILAGRDLVAQHLNVEKSSSSRDA
LVKALYGRLFLWLVKKINNVLCEERKAYFIGVLDIEGFEIFKVNSFEQLCINYTNEKLQQ
FFNHHMFKLEQEEYLKEKINWTFIDFGLDSQATIDLIDGRQPPGILALLDEQSVFPNATD
NTLITKLHSHFSKKNAKYEEPRFSKTEFGVTHYAGQVMYEIQDWLEKNKDPLQQDLELCF
KDSSDNVVTKLFNDPNIASRAKKGANFITVAAQYKEQLASLMATLETTNPHFVRCIIPNN
KQLPAKLEDKVVLDQLRCNGVLEGIRITRKGFPNRIIYADFVKRYYLLAPNVPRDAEDSQ
KATDAVLKHLNIDPEQFRFGITKIFFRAGQLARIEEARELRGDYKDDDDK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
BEF	Beryllium trifluoride ion	Be F3	1

Water and common crystallization additives (EDO) are not listed.

Primary citation

Structure-Function Analysis of Myosin II Backdoor Mutants. Morris, C.A., Coureux, P.-D., Wells, A.L. et al. To be published.

Other PDB entries of the same protein (UniProt P08799 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1W9I 1.75 Å, Myosin II Dictyostelium discoideum motor domain S456Y bound with MgADP-BeFx
3MYK 1.84 Å, Insights into the Importance of Hydrogen Bonding in the Gamma-Phosphate Binding Pocket…
6Z7T 1.88 Å, Nucleotide-free Myosin-II motor domain
1LVK 1.9 Å, X-ray crystal structure of the MG (DOT) 2'(3')-O-(N-methylanthraniloyl) nucleotide bound…
1VOM 1.9 Å, Complex between dictyostelium myosin and mgadp and vanadate at 1.9A resolution
2AKA 1.9 Å, Structure of the nucleotide-free myosin II motor domain from Dictyostelium discoideum…
1W9L 1.95 Å, Myosin II Dictyostelium discoideum motor domain S456E bound with MgADP-AlF4
1D0X 2.0 Å, Dictyostelium myosin S1DC (motor domain fragment) complexed with M-nitrophenyl…
1D0Y 2.0 Å, Dictyostelium myosin S1DC (motor domain fragment) complexed with O-nitrophenyl…
1D0Z 2.0 Å, Dictyostelium myosin S1DC (motor domain fragment) complexed with P-nitrophenyl…
1D1A 2.0 Å, Dictyostelium myosin S1DC (motor domain fragment) complexed with o,p-dinitrophenyl…
1D1B 2.0 Å, Dictyostelium myosin S1DC (motor domain fragment) complexed with o,p-dinitrophenyl…

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