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Crystal Structure of Turtle Cadherin-23 EC1-2

Analyse Crystal Structure of Turtle Cadherin-23 EC1-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7SGX
Type: protein
Length: 826 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.13
Source: Chelonia mydas
Molecule: Cadherin 23
Ligands: CA, CL
Pockets: 2 · best druggability 0.68

Structure

x-ray diffraction · resolution 3.13 · 2 distinct chains · 2% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Cadherin 23	protein	206	3% helix, 46% strand	—
D	Cadherin 23	protein	208	1% helix, 45% strand	—

Ligands and binding sites

CA · Calcium ion · metal · 31 copies · chains A, B, C, D
CL · Chloride ion · ion · 2 copies · chains A, D
GOL · Glycerol · additive · 2 copies · chains A, D

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

Pockets

2 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	549	0.68	0.78	42	empty
2	400	0.56	0.74	47	empty

Interfaces

4 interfaces between chains.

B–D · 494 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 485 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 364 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 218 Å² buried · 1 hydrogen bond · protein-protein

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 7SGX · PDBe 7SGX

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