MolNFT v1 · #121150 · protein

Myosin vc pre-powerstroke state

5HMP · Unconventional myosin-vc: “Myosin vc pre-powerstroke state”. X-ray diffraction, 3 ligands (ADP, MG, VO4), 17 pockets (best druggability 0.68). MolNFT v1 #121150 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5HMP
Type: protein
Length: 1,409 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Unconventional myosin-vc
UniProt: Q9NQX4
Ligands: ADP, MG, VO4
Pockets: 17 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Unconventional myosin-vc	protein	697	44% helix, 16% strand	Q9NQX4
B	Unconventional myosin-vc	protein	712	44% helix, 16% strand	Q9NQX4

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
VO4 · Vanadate ion · ion · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
DMS · Dimethyl sulfoxide · additive · chains A

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

Pockets

17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	480	0.68	0.79	59	MG, VO4, ADP
2	503	0.67	0.78	57	MG, VO4, ADP, EDO
3	66	0.66	0.93	16	empty
4	364	0.64	0.79	49	empty
5	586	0.63	0.75	84	empty

Interfaces

1 interface between chains.

A–B · 722 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

5HMP · Myosin Vc pre-powerstroke state · the same entry in another collection · chain A against A, TM-score 1.00
Q9NQX4 · AlphaFold monomer V2.0 prediction for unconventional myosin-vc (Q9NQX4) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 Q9NQX4
Elsewhere: RCSB PDB 5HMP · PDBe 5HMP · UniProt Q9NQX4

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