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Calcium-bound C2A domain from human dysferlin

Analyse Calcium-bound C2A domain from human dysferlin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JOF
Type: protein
Length: 496 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Isoform 6 of dysferlin
UniProt: O75923
Ligands: CA
Pockets: 4 · best druggability 0.70

Structure

x-ray diffraction · 4 distinct chains · 3% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Isoform 6 of dysferlin	protein	122	2% helix, 57% strand	O75923
B	Isoform 6 of dysferlin	protein	126	3% helix, 54% strand	O75923
C	Isoform 6 of dysferlin	protein	122	3% helix, 57% strand	O75923
D	Isoform 6 of dysferlin	protein	126	3% helix, 56% strand	O75923

Ligands and binding sites

CA · Calcium ion · metal · 8 copies · chains A, B, C, D

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1117	0.70	0.74	116	empty
2	291	0.52	0.74	28	empty
3	91	0.43	0.78	19	empty
4	63	0.41	0.80	10	empty

Interfaces

4 interfaces between chains.

B–C · 455 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 295 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 184 Å² buried · 0 hydrogen bonds · protein-protein
C–D · 136 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

7JOF · Calcium-bound C2A Domain from Human Dysferlin · the same entry in another collection · chain D against D, TM-score 1.00
O75923 · AlphaFold monomer V2.0 prediction for dysferlin (O75923) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 O75923
Elsewhere: RCSB PDB 7JOF · PDBe 7JOF · UniProt O75923

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