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Mouse cadherin-6 EC1-2 adhesive fragment

Analyse Mouse cadherin-6 EC1-2 adhesive fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6CGU
Type: protein
Length: 828 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cadherin-6
UniProt: P97326
Ligands: CA
Pockets: 7 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 1% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Cadherin-6	protein	207	1% helix, 47% strand	P97326

Ligands and binding sites

CA · Calcium ion · metal · 14 copies · chains A, B, C, D

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

Pockets

7 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	1185	0.78	0.80	126	empty
2	401	0.68	0.81	45	empty
3	74	0.33	0.75	16	empty
4	59	0.32	0.76	15	empty
5	59	0.31	0.75	16	empty

Interfaces

4 interfaces between chains.

B–C · 1358 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 1341 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 613 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 611 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6CGU · mouse cadherin-6 EC1-2 adhesive fragment · the same entry in another collection · chain D against D, TM-score 1.00
P97326 · AlphaFold monomer V2.0 prediction for cadherin-6 (P97326) · a predicted model of the same protein · chain B against A, TM-score 0.94

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 P97326
Elsewhere: RCSB PDB 6CGU · PDBe 6CGU · UniProt P97326

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