MolNFT v1 · #68763 · protein

Crystal structure of chicken T-cadherin EC1 EC2

3K5S · Cadherin-13: “Crystal structure of chicken T-cadherin EC1 EC2”. X-ray diffraction, 1 ligand (CA), 3 pockets (best druggability 0.49). MolNFT v1 #68763 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3K5S
Type: protein
Length: 434 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cadherin-13
UniProt: P33150
Ligands: CA
Pockets: 3 · best druggability 0.49

Structure

x-ray diffraction · 1 distinct chain · 1% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cadherin-13	protein	217	1% helix, 44% strand	P33150

Ligands and binding sites

CA · Calcium ion · metal · 6 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	167	0.49	0.77	21	empty
2	106	0.46	0.79	24	empty
3	122	0.43	0.77	21	empty

Interfaces

1 interface between chains.

A–B · 1067 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

3K5S · Crystal structure of chicken T-cadherin EC1 EC2 · the same entry in another collection · chain A against A, TM-score 1.00
P33150 · AlphaFold monomer V2.0 prediction for cadherin-13 (P33150) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 P33150
Elsewhere: RCSB PDB 3K5S · PDBe 3K5S · UniProt P33150

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