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Crystal structure of human protocadherin-24 EC1-2

Analyse Crystal structure of human protocadherin-24 EC1-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5CZR
Type: protein
Length: 863 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cadherin-related family member 2
UniProt: Q9BYE9
Ligands: CA
Pockets: 8 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cadherin-related family member 2	protein	215	7% helix, 46% strand	Q9BYE9
B, D	Cadherin-related family member 2	protein	216	6% helix, 46% strand	Q9BYE9
C	Cadherin-related family member 2	protein	216	6% helix, 46% strand	Q9BYE9

Ligands and binding sites

CA · Calcium ion · metal · 16 copies · chains A, B, C, D

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

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	579	0.77	0.83	70	empty
2	233	0.67	0.84	32	empty
3	390	0.67	0.80	35	empty
4	256	0.64	0.82	36	empty
5	402	0.59	0.76	40	empty

Interfaces

6 interfaces between chains.

A–D · 1058 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 1011 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 306 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 260 Å² buried · 1 hydrogen bond · protein-protein
A–C · 234 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5CZR · Crystal Structure of Human Protocadherin-24 EC1-2 · the same entry in another collection · chain A against A, TM-score 1.00
Q9BYE9 · AlphaFold monomer V2.0 prediction for cadherin-related family member 2 (Q9BYE9) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q9BYE9
Elsewhere: RCSB PDB 5CZR · PDBe 5CZR · UniProt Q9BYE9

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