MolNFT v1 · #117159 · protein

Protocadherin alpha 7 extracellular cadherin domains 1-5

5DZV · Protein PCDHA7: “Protocadherin alpha 7 extracellular cadherin domains 1-5”. X-ray diffraction, 5 ligands (MAN, NAG, FUC), 11 pockets (best druggability 0.69). MolNFT v1 #117159 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5DZV
Type: protein
Length: 1,043 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein PCDHA7
UniProt: Q91Y13
Ligands: MAN, NAG, FUC, BMA, CA
Pockets: 11 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein PCDHA7	protein	521	6% helix, 43% strand	Q91Y13
B	Protein PCDHA7	protein	522	6% helix, 42% strand	Q91Y13

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 8 copies · chains B, A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 2 copies
CA · Calcium ion · metal · 24 copies · chains A, B

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

Pockets

11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	300	0.69	0.83	44	empty
2	238	0.68	0.84	32	empty
3	388	0.66	0.80	59	empty
4	376	0.66	0.80	64	empty
5	532	0.64	0.76	63	empty

Interfaces

1 interface between chains.

A–B · 1789 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 glycan, 2 disulfide (O-glycosylation, N-glycosylation, disulfide).

Compared structures

5DZV · Protocadherin alpha 7 extracellular cadherin domains 1-5 · the same entry in another collection · chain A against A, TM-score 1.00
Q91Y13 · AlphaFold monomer V2.0 prediction for protocadherin alpha-7 (Q91Y13) · a predicted model of the same protein · chain B against A, TM-score 0.94

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 Q91Y13
Elsewhere: RCSB PDB 5DZV · PDBe 5DZV · UniProt Q91Y13

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