Research workbench

Crystal structure of squid MG.ADP myosin S1

Analyse Crystal structure of squid MG.ADP myosin S1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3I5F
Type: protein
Length: 1,114 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Myosin heavy chain isoform a; Myosin regulatory light chain lc-2, mantle muscle; Myosin…
UniProt: O44934, P08052, P05945
Ligands: ADP, MG
Pockets: 14 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Myosin heavy chain isoform a	protein	810	49% helix, 11% strand	O44934
B	Myosin regulatory light chain lc-2, mantle muscle	protein	145	52% helix, 1% strand	P08052
C	Myosin catalytic light chain lc-1, mantle muscle	protein	159	52% helix, 4% strand	P05945

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
MG · Magnesium ion · metal · chains A

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

Pockets

14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1131	0.81	0.82	136	MG, ADP
2	990	0.80	0.81	95	empty
3	263	0.70	0.85	40	empty
4	158	0.53	0.80	29	empty
5	208	0.48	0.75	31	empty

Interfaces

3 interfaces between chains.

A–C · 2092 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1942 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 235 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3I5F · Crystal structure of squid MG.ADP myosin S1 · the same entry in another collection · chain A against A, TM-score 1.00
P08052 · AlphaFold monomer V2.0 prediction for myosin regulatory light chain lc-2, mantle muscle… · a predicted model of the same protein · chain B against A, TM-score 0.63

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 O44934
Every structure of UniProt P08052
Every structure of UniProt P05945
Elsewhere: RCSB PDB 3I5F · PDBe 3I5F · UniProt O44934 · UniProt P08052 · UniProt P05945

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