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Crystal structure of drosophila numb ptb domain and pon peptide complex

Analyse Crystal structure of drosophila numb ptb domain and pon peptide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YI7
Type: protein
Length: 293 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein numb; Pon peptide from partner of numb
UniProt: P16554, Q9W4I7
Pockets: 1 · best druggability 0.39

Structure

x-ray diffraction · 3 distinct chains · 29% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein numb	protein	128	30% helix, 42% strand	P16554
B, D	Pon peptide from partner of numb	protein	17	0% helix, 12% strand	Q9W4I7
C	Protein numb	protein	131	32% helix, 41% strand	P16554

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	129	0.39	0.74	23	empty

Interfaces

4 interfaces between chains.

C–D · 548 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 544 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 167 Å² buried · 1 hydrogen bond · protein-protein
A–D · 110 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5YI7 · Crystal structure of drosophila Numb PTB domain and Pon peptide complex · the same entry in another collection · chain A against A, TM-score 1.00
P16554 · AlphaFold monomer V2.0 prediction for protein numb (P16554) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P16554
Every structure of UniProt Q9W4I7
Elsewhere: RCSB PDB 5YI7 · PDBe 5YI7 · UniProt P16554 · UniProt Q9W4I7

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