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Crystal structures of human pyy and npy

Analyse Crystal structures of human pyy and npy in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7RT9
Type: protein
Length: 907 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 4A3B2-a Fab heavy chain; 4A3B2-a Fab light chain; Peptide yy
UniProt: P10082
Ligands: NH2
Pockets: 6 · best druggability 0.67

Structure

x-ray diffraction · 6 distinct chains · 11% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	4A3B2-a Fab heavy chain	protein	204	6% helix, 52% strand	—
B	4A3B2-a Fab light chain	protein	212	7% helix, 50% strand	—
C	4A3B2-a Fab heavy chain	protein	207	9% helix, 53% strand	—
D	4A3B2-a Fab light chain	protein	213	6% helix, 50% strand	—
Y	Peptide yy	protein	36	56% helix, 0% strand	P10082
Z	Peptide yy	protein	35	57% helix, 0% strand	P10082

Ligands and binding sites

NH2 · Amino group · ion · 2 copies · chains A, Y, C, Z
GOL · Glycerol · additive · 2 copies · chains A, Y

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	809	0.67	0.74	84	empty
2	542	0.62	0.75	66	empty
3	54	0.55	0.90	22	empty
4	55	0.47	0.86	22	empty
5	100	0.42	0.78	17	empty

Interfaces

8 interfaces between chains.

C–D · 1543 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 1500 Å² buried · 9 hydrogen bonds · protein-protein
A–Y · 379 Å² buried · 4 hydrogen bonds · protein-protein
C–Z · 350 Å² buried · 3 hydrogen bonds · protein-protein
B–Y · 329 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

7RT9 · Crystal structures of human PYY and NPY · the same entry in another collection · chain Y against Y, TM-score 1.00
P10082 · AlphaFold monomer V2.0 prediction for peptide yy (P10082) · a predicted model of the same protein · chain Z against A, TM-score 0.80

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 P10082
Elsewhere: RCSB PDB 7RT9 · PDBe 7RT9 · UniProt P10082

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