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The crystal structure of H-2DB with a S-glutathionylated peptide

Analyse The crystal structure of H-2DB with a S-glutathionylated peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4PG2
Type: protein
Length: 363 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class I histocompatibility antigen, D-B alpha chain; Beta-2-microglobulin…
UniProt: P01899, P01887
Ligands: GSH, SO4
Pockets: 4 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, D-B alpha chain	protein	254	29% helix, 38% strand	P01899
C	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P01887
D	Cys-ser-leu-TRP-asn-gly-pro-his-leu	protein	9	0% helix, 0% strand	—

Ligands and binding sites

GSH · Glutathione · ligand · chains A, D
SO4 · Sulfate ion · ion · 4 copies · chains A, C, D

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

Pockets

4 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	576	0.66	0.77	55	empty
2	136	0.48	0.78	30	empty
3	100	0.47	0.80	17	empty
4	65	0.39	0.80	17	empty

Interfaces

2 interfaces between chains.

A–C · 1364 Å² buried · 21 hydrogen bonds · protein-protein
A–D · 915 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

4PG2 · The crystal structure of H-2Db with a S-glutathionylated peptide · the same entry in another collection · chain A against A, TM-score 1.00
P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 P01899
Every structure of UniProt P01887
Elsewhere: RCSB PDB 4PG2 · PDBe 4PG2 · UniProt P01899 · UniProt P01887

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