MolNFT v1 · #137668 · protein

Crystal structure of human CDH23 EC21-23

5VVM · Cadherin-23: “Crystal structure of human CDH23 EC21-23”. X-ray diffraction, 1 ligand (CA), 4 pockets (best druggability 0.56). MolNFT v1 #137668 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5VVM
Type: protein
Length: 612 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cadherin-23
UniProt: Q9H251
Ligands: CA
Pockets: 4 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 2% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cadherin-23	protein	298	2% helix, 39% strand	Q9H251
B	Cadherin-23	protein	314	2% helix, 43% strand	Q9H251

Ligands and binding sites

CA · Calcium ion · metal · 12 copies · chains A, B

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

Pockets

4 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	384	0.56	0.74	45	empty
2	262	0.51	0.75	30	empty
3	80	0.42	0.80	18	empty
4	60	0.35	0.77	12	empty

Interfaces

1 interface between chains.

A–B · 422 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5VVM · Crystal structure of human CDH23 EC21-23 · the same entry in another collection · chain A against A, TM-score 1.00

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 Q9H251
Elsewhere: RCSB PDB 5VVM · PDBe 5VVM · UniProt Q9H251

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