Research workbench

Plasmodium falciparum myosin a delta-nter, post-rigor state

Analyse Plasmodium falciparum myosin a delta-nter, post-rigor state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YCZ
Type: protein
Length: 1,057 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Myosin-a; Myosin a tail domain interacting protein; Uncharacterized protein
UniProt: Q8IDR3, W7K1J7, A0A2I0BQX1
Ligands: ADP, MG, SO4
Pockets: 10 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 51% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Myosin-a	protein	795	49% helix, 15% strand	Q8IDR3
B	Myosin a tail domain interacting protein	protein	131	60% helix, 9% strand	W7K1J7
C	Uncharacterized protein	protein	131	50% helix, 6% strand	A0A2I0BQX1

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
MG · Magnesium ion · metal · chains A
SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
EDO · 1,2-ethanediol · additive · 2 copies · chains A, C

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

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1066	0.81	0.82	84	SO4
2	1188	0.78	0.80	115	SO4
3	1122	0.76	0.79	76	EDO
4	364	0.63	0.79	47	empty
5	390	0.63	0.78	45	MG, ADP

Interfaces

3 interfaces between chains.

A–C · 2085 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1451 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 371 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6YCZ · Plasmodium falciparum Myosin A delta-Nter, Post-Rigor state · the same entry in another collection · chain A against A, TM-score 1.00
Q8IDR3 · AlphaFold monomer V2.0 prediction for myosin-a (Q8IDR3) · a predicted model of the same protein · chain A against A, TM-score 0.91

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 Q8IDR3
Every structure of UniProt W7K1J7
Every structure of UniProt A0A2I0BQX1
Elsewhere: RCSB PDB 6YCZ · PDBe 6YCZ · UniProt Q8IDR3 · UniProt W7K1J7 · UniProt A0A2I0BQX1

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