MolNFT v1 · #73482 · protein

Human class I MHC HLA-A2 in complex with the peptidomimetic ela-1.1

3O3B · HLA class I histocompatibility antigen, a-2 alpha chain: “Human class I MHC HLA-A2 in complex with the peptidomimetic ela-1.1”. X-ray diffraction, 7 pockets (best druggability 0.78). MolNFT v1 #73482 on GenesisL1: 3D structure…

PDB: 3O3B
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: 7 · 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, 40% strand	P01892
B, E	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, F	Peptidomimetic ela-1.1	protein	8	0% helix, 0% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 10 copies · chains A, B, C, D, E, F

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1129	0.78	0.80	90	GOL
2	806	0.74	0.79	74	GOL
3	147	0.53	0.80	29	GOL
4	145	0.52	0.80	30	GOL
5	120	0.45	0.78	19	empty

Interfaces

6 interfaces between chains.

D–E · 1409 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1398 Å² buried · 19 hydrogen bonds · protein-protein
D–F · 856 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 851 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 621 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

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

Compared structures

3O3B · Human Class I MHC HLA-A2 in complex with the Peptidomimetic ELA-1.1 · the same entry in another collection · chain E against E, 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 3O3B · PDBe 3O3B · UniProt P01892 · UniProt P61769

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