Research workbench

X-ray structure of the canonical C2A domain from human dysferlin

Analyse X-ray structure of the canonical 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: 4IHB
Type: protein
Length: 759 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dysferlin
UniProt: O75923
Ligands: CA
Pockets: 5 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 3% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E, F	Dysferlin	protein	126	5% helix, 55% strand	O75923
C	Dysferlin	protein	127	2% helix, 54% strand	O75923
D	Dysferlin	protein	128	2% helix, 56% strand	O75923

Ligands and binding sites

CA · Calcium ion · metal · chains E
FMT · Formic acid · additive · 39 copies · chains A, F, B, C, D, E

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

Pockets

5 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	618	0.74	0.81	70	FMT
2	643	0.72	0.79	65	FMT
3	284	0.56	0.76	39	FMT
4	350	0.54	0.74	49	FMT
5	88	0.34	0.74	17	FMT

Interfaces

9 interfaces between chains.

D–E · 526 Å² buried · 3 hydrogen bonds · protein-protein
E–F · 492 Å² buried · 1 hydrogen bond · protein-protein
B–C · 445 Å² buried · 5 hydrogen bonds · protein-protein
D–F · 445 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 430 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4IHB · X-RAY STRUCTURE OF THE canonical C2A DOMAIN FROM HUMAN DYSFERLIN · the same entry in another collection · chain F against F, TM-score 1.00
O75923 · AlphaFold monomer V2.0 prediction for dysferlin (O75923) · a predicted model of the same protein · chain B against A, TM-score 0.93

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 4IHB · PDBe 4IHB · UniProt O75923

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