Research workbench

Human class I MHC HLA-A2(A150P) in complex with the tax peptide

Analyse Human class I MHC HLA-A2(A150P) in complex with the tax peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3IXA
Type: protein
Length: 768 residues
Chains: 6
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; Tax peptide
UniProt: P01892, P61769
Pockets: 8 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	HLA class I histocompatibility antigen, a-2 alpha chain	protein	275	27% helix, 39% strand	P01892
B, E	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, F	Tax peptide	protein	9	0% helix, 0% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 4 copies · chains A, B, D, E

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

Pockets

8 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	1009	0.77	0.79	77	GOL
2	734	0.71	0.78	66	empty
3	182	0.49	0.77	25	empty
4	128	0.48	0.79	24	GOL
5	106	0.47	0.80	29	GOL

Interfaces

5 interfaces between chains.

A–B · 1442 Å² buried · 21 hydrogen bonds · protein-protein
D–E · 1413 Å² buried · 21 hydrogen bonds · protein-protein
D–F · 901 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 900 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 568 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3IXA · Human Class I MHC HLA-A2(A150P) in complex with the Tax peptide · the same entry in another collection · chain F against F, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain E against A, TM-score 0.98

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
Elsewhere: RCSB PDB 3IXA · PDBe 3IXA · UniProt P01892 · UniProt P61769

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