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Crystal structure of mouse P-cadherin extracellular domains EC1-EC2

Analyse Crystal structure of mouse P-cadherin extracellular domains EC1-EC2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4NQQ
Type: protein
Length: 847 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cadherin-3
UniProt: P10287
Ligands: CA, CU
Pockets: 4 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 3% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cadherin-3	protein	213	3% helix, 45% strand	P10287
C	Cadherin-3	protein	210	3% helix, 47% strand	P10287
D	Cadherin-3	protein	211	3% helix, 45% strand	P10287

Ligands and binding sites

CA · Calcium ion · metal · 14 copies · chains A, B, C, D
CU · Copper (II) ion · metal · 9 copies · chains A, C, B, 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	617	0.78	0.84	55	empty
2	68	0.70	0.96	18	empty
3	500	0.66	0.77	47	empty
4	180	0.46	0.75	31	empty

Interfaces

3 interfaces between chains.

A–B · 901 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 506 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 488 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4NQQ · Crystal structure of mouse P-cadherin extracellular domains EC1-EC2 · the same entry in another collection · chain D against D, TM-score 1.00
P10287 · AlphaFold monomer V2.0 prediction for cadherin-3 (P10287) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 P10287
Elsewhere: RCSB PDB 4NQQ · PDBe 4NQQ · UniProt P10287

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