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Crystal structure of the pH domain of sharpin

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

PDB: 4EMO
Type: protein
Length: 426 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sharpin
UniProt: Q9H0F6
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 4 distinct chains · 19% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sharpin	protein	104	19% helix, 43% strand	Q9H0F6
B	Sharpin	protein	100	20% helix, 46% strand	Q9H0F6
C	Sharpin	protein	117	19% helix, 41% strand	Q9H0F6
D	Sharpin	protein	105	17% helix, 42% strand	Q9H0F6

Pockets

4 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	348	0.67	0.81	52	empty
2	262	0.57	0.78	42	empty
3	153	0.43	0.75	26	empty
4	69	0.31	0.74	16	empty

Interfaces

5 interfaces between chains.

B–C · 929 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 661 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 632 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 343 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 127 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 9 modified (engineered).

Compared structures

4EMO · Crystal structure of the PH domain of SHARPIN · the same entry in another collection · chain D against D, TM-score 1.00
Q9H0F6 · AlphaFold monomer V2.0 prediction for sharpin (Q9H0F6) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q9H0F6
Elsewhere: RCSB PDB 4EMO · PDBe 4EMO · UniProt Q9H0F6

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