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Unusual structural features in the adduct of dirhodium tetraacetate with lysozyme (5)

Analyse Unusual structural features in the adduct of dirhodium tetraacetate with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7BEC
Type: protein
Length: 129 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.74
Source: Gallus gallus
Molecule: Lysozyme
EC: 3.2.1.17
UniProt: P00698
Ligands: RH, NA, NO3
Pockets: 1 · best druggability 0.34

Structure

x-ray diffraction · resolution 1.74 · 1 distinct chain · 41% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
AAA	Lysozyme (EC 3.2.1.17)	protein	129	41% helix, 11% strand	P00698

Ligands and binding sites

RH · Rhodium · metal · 3 copies · chains AAA
NA · Sodium ion · metal · chains AAA
NO3 · Nitrate ion · ion · 5 copies · chains AAA
ACT · Acetate ion · additive · 2 copies · chains AAA
EDO · 1,2-ethanediol · additive · chains AAA

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	64	0.34	0.76	16	NO3

Modifications

Observed in the structure: 4 disulfide (disulfide).

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 P00698
Elsewhere: RCSB PDB 7BEC · PDBe 7BEC · UniProt P00698

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