MolNFT v1 · #140614 · protein

Crystal structure of drosophila melanogaster papi extended tudor domain (D287A) in complex with piwi N-terminal R10-unme peptide

5YGF · GH18329P: “Crystal structure of drosophila melanogaster papi extended tudor domain (D287A) in complex with piwi…”. X-ray diffraction, 2 pockets (best druggability 0.67). MolNFT v1 #140614 on GenesisL1: 3D structure, binding sites…

PDB: 5YGF
Type: protein
Length: 224 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GH18329P; Asp-gln-gly-arg-gly-arg-arg-arg-pro
UniProt: Q9VQ91
Pockets: 2 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 22% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GH18329P	protein	215	23% helix, 34% strand	Q9VQ91
D	Asp-gln-gly-arg-gly-arg-arg-arg-pro	protein	9	0% helix, 11% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	419	0.67	0.80	53	empty
2	72	0.44	0.81	19	empty

Interfaces

1 interface between chains.

A–D · 761 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

5YGF · Crystal structure of Drosophila melanogaster Papi extended Tudor domain (D287A) in… · the same entry in another collection · chain A against A, TM-score 1.00
Q9VQ91 · AlphaFold monomer V2.0 prediction for tudor and kh domain-containing protein homolog… · 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 Q9VQ91
Elsewhere: RCSB PDB 5YGF · PDBe 5YGF · UniProt Q9VQ91

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