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Crystal structure of a ubiquitin-dependent degradation substrate: a three-disulfide form of lysozyme

Analyse Crystal structure of a ubiquitin-dependent degradation substrate: a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1RCM
Type: protein
Length: 258 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hen egg white lysozyme
EC: 3.2.1.17
UniProt: P00698
Pockets: 2 · best druggability 0.32

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Hen egg white lysozyme (EC 3.2.1.17)	protein	129	42% helix, 11% strand	P00698

Ligands and binding sites

ACY · Acetic acid · additive · 2 copies · chains A, B

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

Pockets

2 pockets 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	0.32	0.75	13	empty
2	59	0.30	0.75	15	empty

Interfaces

1 interface between chains.

A–B · 596 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 2 covalent (disulfide, additive adduct).

Compared structures

1RCM · Crystal structure of a ubiquitin-dependent degradation substrate: a three-disulfide form… · 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 P00698
Elsewhere: RCSB PDB 1RCM · PDBe 1RCM · UniProt P00698

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