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Crystal structure of myosin V motor domain - nucleotide-free

Analyse Crystal structure of myosin V motor domain - nucleotide-free in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1W8J
Type: protein
Length: 2,880 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Myosin va
UniProt: Q02440
Ligands: SO4
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 44% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Myosin va	protein	722	44% helix, 15% strand	Q02440
B	Myosin va	protein	718	44% helix, 17% strand	Q02440
C	Myosin va	protein	723	44% helix, 17% strand	Q02440
D	Myosin va	protein	717	43% helix, 15% strand	Q02440

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, B, D

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	736	0.75	0.80	76	empty
2	690	0.73	0.79	62	empty
3	636	0.73	0.80	82	SO4
4	711	0.73	0.79	60	empty
5	640	0.73	0.80	59	empty

Interfaces

1 interface between chains.

B–D · 62 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1W8J · Crystal Structure Of Myosin V Motor Domain - Nucleotide-Free · the same entry in another collection · chain D against D, TM-score 1.00
Q02440 · AlphaFold monomer V2.0 prediction for unconventional myosin-va (Q02440) · a predicted model of the same protein · chain D against A, TM-score 0.96

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 Q02440
Elsewhere: RCSB PDB 1W8J · PDBe 1W8J · UniProt Q02440

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