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Crystal structure of the extended tudor domain from bmpapi

Analyse Crystal structure of the extended tudor domain from bmpapi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VY1
Type: protein
Length: 389 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tudor and kh domain-containing protein homolog
UniProt: H9JD76
Pockets: 2 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 25% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tudor and kh domain-containing protein homolog	protein	204	24% helix, 38% strand	H9JD76
B	Tudor and kh domain-containing protein homolog	protein	185	26% helix, 39% strand	H9JD76

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1110	0.80	0.81	80	empty
2	179	0.51	0.77	27	empty

Interfaces

1 interface between chains.

A–B · 816 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5VY1 · Crystal structure of the extended Tudor domain from BmPAPI · the same entry in another collection · chain A against A, TM-score 1.00
H9JD76 · AlphaFold monomer V2.0 prediction for tudor and kh domain-containing protein homolog… · a predicted model of the same protein · chain B against A, TM-score 0.98

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 H9JD76
Elsewhere: RCSB PDB 5VY1 · PDBe 5VY1 · UniProt H9JD76

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