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Domain characterization of the wd protein PWP2 and their relevance in ribosome biogenesis

Analyse Domain characterization of the wd protein PWP2 and their relevance in ribosome… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5I2T
Type: protein
Length: 606 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Periodic tryptophan protein 2
UniProt: P25635
Ligands: SO4
Pockets: 4 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 0% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Periodic tryptophan protein 2	protein	606	0% helix, 51% strand	P25635

Ligands and binding sites

SO4 · Sulfate ion · ion · chains A

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

Pockets

4 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	864	0.81	0.83	63	empty
2	640	0.77	0.83	57	empty
3	134	0.59	0.84	29	empty
4	82	0.33	0.74	15	empty

Compared structures

5I2T · Domain characterization of the WD protein Pwp2 and their relevance in ribosome biogenesis · the same entry in another collection · chain A against A, TM-score 1.00
P25635 · AlphaFold monomer V2.0 prediction for periodic tryptophan protein 2 (P25635) · a predicted model of the same protein · chain A against A, TM-score 0.89

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 P25635
Elsewhere: RCSB PDB 5I2T · PDBe 5I2T · UniProt P25635

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