Research workbench

Human class I MHC HLA-A2 in complex with the peptidomimetic ela-2

Analyse Human class I MHC HLA-A2 in complex with the peptidomimetic ela-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3O3D
Type: protein
Length: 766 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…
UniProt: P01892, P61769
Pockets: 11 · best druggability 0.78

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	28% helix, 39% strand	P01892
B, E	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, F	Peptidomimetic ela-2	protein	8	0% helix, 0% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 5 copies · chains A, B, D, E

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

Pockets

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	994	0.78	0.80	86	GOL
2	661	0.73	0.79	73	GOL
3	82	0.62	0.90	17	empty
4	78	0.61	0.89	17	empty
5	160	0.53	0.79	31	GOL

Interfaces

5 interfaces between chains.

A–B · 1429 Å² buried · 19 hydrogen bonds · protein-protein
D–E · 1405 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 812 Å² buried · 15 hydrogen bonds · protein-protein
D–F · 799 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 589 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 4 modified (disulfide, nonstandard).

Compared structures

3O3D · Human Class I MHC HLA-A2 in complex with the Peptidomimetic ELA-2 · the same entry in another collection · chain D against D, 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

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 3O3D · PDBe 3O3D · UniProt P01892 · UniProt P61769

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