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Crystal structure of the ubx domain of human UBXD7

Analyse Crystal structure of the ubx domain of human UBXD7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5X3P
Type: protein
Length: 237 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubx domain-containing protein 7
UniProt: O94888
Pockets: 3 · best druggability 0.52

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubx domain-containing protein 7	protein	80	21% helix, 39% strand	O94888
B	Ubx domain-containing protein 7	protein	79	13% helix, 39% strand	O94888
C	Ubx domain-containing protein 7	protein	78	22% helix, 40% strand	O94888

Pockets

3 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	193	0.52	0.77	25	empty
2	134	0.41	0.75	22	empty
3	80	0.40	0.79	20	empty

Interfaces

3 interfaces between chains.

A–B · 502 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 430 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 415 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified, 1 disulfide (engineered, disulfide).

Compared structures

5X3P · Crystal structure of the UBX domain of human UBXD7 · the same entry in another collection · chain A against A, TM-score 1.00
O94888 · AlphaFold monomer V2.0 prediction for ubx domain-containing protein 7 (O94888) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 O94888
Elsewhere: RCSB PDB 5X3P · PDBe 5X3P · UniProt O94888

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