Research workbench

Crystal structure of rty phosphopeptide bound to human class I MHC HLA-A2

Analyse Crystal structure of rty phosphopeptide bound to human class I MHC HLA-A2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3BH9
Type: protein
Length: 385 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin; Decameric…
UniProt: P01892, P61769, Q8WVV4
Ligands: NA
Pockets: 3 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, a-2 alpha chain	protein	275	27% helix, 40% strand	P01892
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	Decameric peptide from protein POF1B	protein	10	0% helix, 0% strand	Q8WVV4

Ligands and binding sites

NA · Sodium ion · metal · chains A
EDO · 1,2-ethanediol · additive · 2 copies · chains B, A, C

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

Pockets

3 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	614	0.68	0.77	55	empty
2	131	0.46	0.77	20	empty
3	80	0.39	0.78	18	empty

Interfaces

2 interfaces between chains.

A–B · 1387 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 923 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 1 modified (disulfide, phosphorylation).

Compared structures

3BH9 · Crystal Structure of RTY Phosphopeptide Bound to Human Class I MHC HLA-A2 · the same entry in another collection · chain A against A, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
Q8WVV4 · AlphaFold monomer V2.0 prediction for protein POF1B (Q8WVV4) · a predicted model of the same protein · chain C against A, TM-score 0.30

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 P01892
Every structure of UniProt P61769
Every structure of UniProt Q8WVV4
Elsewhere: RCSB PDB 3BH9 · PDBe 3BH9 · UniProt P01892 · UniProt P61769 · UniProt Q8WVV4

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