MolNFT v1 · #40590 · protein

Structure of apo-calmodulin bound to unconventional myosin V

2IX7: “Structure of apo-calmodulin bound to unconventional myosin V”. X-ray diffraction, 2 ligands (CYS, SO4), 4 pockets (best druggability 0.45). MolNFT v1 #40590 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2IX7
Type: protein
Length: 348 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Calmodulin; Myosin-5A
UniProt: P62204, Q99104
Ligands: CYS, SO4
Pockets: 4 · best druggability 0.45

Structure

x-ray diffraction · 2 distinct chains · 67% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Calmodulin	protein	145	57% helix, 7% strand	P62204
C	Myosin-5A	protein	58	93% helix, 0% strand	Q99104

Ligands and binding sites

CYS · Cysteine · ligand · chains B, C
SO4 · Sulfate ion · ion · 5 copies · chains B, A, C

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	110	0.45	0.79	22	empty
2	50	0.37	0.80	14	empty
3	91	0.35	0.74	15	empty
4	84	0.32	0.73	17	empty

Interfaces

3 interfaces between chains.

A–C · 1484 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 1474 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 257 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

2IX7 · Structure of apo-calmodulin bound to unconventional myosin V · the same entry in another collection · chain A against A, TM-score 1.00
Q99104 · AlphaFold monomer V2.0 prediction for unconventional myosin-va (Q99104) · a predicted model of the same protein · chain C 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 P62204
Every structure of UniProt Q99104
Elsewhere: RCSB PDB 2IX7 · PDBe 2IX7 · UniProt P62204 · UniProt Q99104

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