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Crystal structure of an uncharacterized protein

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

PDB: 6INY
Type: protein
Length: 460 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.997
Source: Escherichia coli
Molecule: UPF0061 protein YdiU
UniProt: A0A024L327
Ligands: ANP, MG
Pockets: 4 · best druggability 0.64

Structure

x-ray diffraction · resolution 1.997 · 1 distinct chain · 44% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	UPF0061 protein YdiU	protein	460	44% helix, 16% strand	A0A024L327

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
MG · Magnesium ion · metal · 2 copies · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	434	0.64	0.78	43	ANP, MG
2	138	0.58	0.83	26	empty
3	130	0.44	0.76	23	empty
4	138	0.38	0.73	28	empty

Modifications

Observed in the structure: 14 modified (engineered).

Compared structures

6INY · Crystal structure of an uncharacterized protein · the same entry in another collection · chain A against A, TM-score 1.00

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 A0A024L327
Elsewhere: RCSB PDB 6INY · PDBe 6INY · UniProt A0A024L327

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