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Crystal structure of human P-cadherin (ss-X-dimer)

Analyse Crystal structure of human P-cadherin (ss-X-dimer) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ZMQ
Type: protein
Length: 414 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cadherin-3
UniProt: P22223
Ligands: CA
Pockets: 2 · best druggability 0.61

Structure

x-ray diffraction · 2 distinct chains · 2% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cadherin-3	protein	200	2% helix, 47% strand	P22223
B	Cadherin-3	protein	214	2% helix, 45% strand	P22223

Ligands and binding sites

CA · Calcium ion · metal · 8 copies · chains A, B
1PE · Pentaethylene glycol · additive · chains A

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	235	0.61	0.81	30	empty
2	221	0.59	0.80	33	empty

Interfaces

1 interface between chains.

A–B · 1866 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

4ZMQ · Crystal structure of human P-cadherin (ss-X-dimer) · the same entry in another collection · chain A against A, TM-score 1.00
P22223 · AlphaFold monomer V2.0 prediction for cadherin-3 (P22223) · a predicted model of the same protein · chain A 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 P22223
Elsewhere: RCSB PDB 4ZMQ · PDBe 4ZMQ · UniProt P22223

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