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Human P-cadherin MEC1 with scfv TSP7 bound

Analyse Human P-cadherin MEC1 with scfv TSP7 bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5JYL
Type: protein
Length: 645 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cadherin-3; Scfv TSP7
UniProt: P22223
Ligands: CL, PO4
Pockets: 8 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 5% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cadherin-3	protein	97	0% helix, 42% strand	P22223
B	Scfv TSP7	protein	230	7% helix, 50% strand	—
C	Cadherin-3	protein	96	0% helix, 43% strand	P22223
D	Scfv TSP7	protein	222	7% helix, 48% strand	—

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains B, D
PO4 · Phosphate ion · ion · chains B
GOL · Glycerol · additive · chains A, B

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

Pockets

8 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	1055	0.75	0.78	113	empty
2	55	0.50	0.86	18	empty
3	134	0.45	0.77	24	empty
4	119	0.42	0.76	27	empty
5	106	0.40	0.76	24	empty

Interfaces

5 interfaces between chains.

C–D · 771 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 760 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 455 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 315 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 275 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5JYL · Human P-cadherin MEC1 with scFv TSP7 bound · 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 C against A, TM-score 0.96

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 5JYL · PDBe 5JYL · UniProt P22223

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