1D1B: Dictyostelium myosin S1DC

Dictyostelium myosin S1DC (motor domain fragment) complexed with o,p-dinitrophenyl aminopropyldiphosphate beryllium trifluoride. Determined by X-ray diffraction at 2.0 Å resolution. Released 12 Jan 2000.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Dictyostelium discoideum
Chains: 1
Atoms: 6,374
Mol. weight: 87.23 kDa
Ligands: MG, DAQ
Released: 12 Jan 2000

Explore 1D1B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1D1B contains 37 α-helices and 29 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: 37 helices, 29 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
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	290-296	7
α-helix	301-303	3
α-helix	320-334	15
α-helix	338-355	18
α-helix	357-359	3
β-strand	360-361	2	4
β-strand	367-368	2	4
α-helix	373-382	10
α-helix	386-394	9
β-strand	397-399	3	5
β-strand	404-406	3	5
α-helix	411-441	31
β-strand	448-454	7	2
β-strand	464	1	6
α-helix	466-489	24
α-helix	491-493	3
α-helix	506-508	3
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	681-689	9
β-strand	694	1	7
β-strand	697	1	8
α-helix	698-705	8
α-helix	719-729	11
α-helix	734-736	3
β-strand	737-739	3	7
β-strand	743	1	8
β-strand	744-746	3	7
α-helix	750-755	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Myosin	A	protein	761	Dictyostelium discoideum	P08799 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1D1B_1 MYOSIN (chains A)
MNPIHDRTSDYHKYLKVKQGDSDLFKLTVSDKRYIWYNPDPKERDSYECGEIVSETSDSF
TFKTVDGQDRQVKKDDANQRNPIKFDGVEDMSELSYLNEPAVFHNLRVRYNQDLIYTYSG
LFLVAVNPFKRIPIYTQEMVDIFKGRRRNEVAPHIFAISDVAYRSMLDDRQNQSLLITGE
SGAGKTENTKKVIQYLASVAGRNQANGSGVLEQQILQANPILEAFGNAKTTRNNNSSRFG
KFIEIQFNNAGFISGASIQSYLLEKSRVVFQSETERNYHIFYQLLAGATAEEKKALHLAG
PESFNYLNQSGCVDIKGVSDSEEFKITRQAMDIVGFSQEEQMSIFKIIAGILHLGNIKFE
KGAGEGAVLKDKTALNAASTVFGVNPSVLEKALMEPRILAGRDLVAQHLNVEKSSSSRDA
LVKALYGRLFLWLVKKINNVLCQERKAYFIGVLDISGFEIFKVNSFEQLCINYTNEKLQQ
FFNHHMFKLEQEEYLKEKINWTFIDFGLDSQATIDLIDGRQPPGILALLDEQSVFPNATD
NTLITKLHSHFSKKNAKYEEPRFSKTEFGVTHYAGQVMYEIQDWLEKNKDPLQQDLELCF
KDSSDNVVTKLFNDPNIASRAKKGANFITVAAQYKEQLASLMATLETTNPHFVRCIIPNN
KQLPAKLEDKVVLDQLRCNGVLEGIRITRKGFPNRIIYADFVKRYYLLAPNVPRDAEDSQ
KATDAVLKHLNIDPEQYRFGITKIFFRAGQLARIEEAREPN

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
DAQ	O,p-dinitrophenyl aminopropyldiphosphate beryllium trifluoride	C9 H12 Be F3 N3 O11 P2	1

Primary citation

X-ray structures of the Dictyostelium discoideum myosin motor domain with six non-nucleotide analogs. Gulick, A.M., Bauer, C.B., Thoden, J.B. et al. J Biol Chem (2000) 275:398-408. DOI 10.1074/jbc.275.1.398 · PubMed

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…
1MMD 2.0 Å, Truncated head of myosin from dictyostelium discoideum complexed with mgadp-BEF3

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