MolNFT v1 · #159439 · protein

Crystal structure of ilnamivki peptide bound to HLA-A2

6OPD · HLA class I histocompatibility antigen, a-2 alpha chain: “Crystal structure of ilnamivki peptide bound to HLA-A2”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.71). MolNFT v1 #159439 on GenesisL1: 3D structure…

PDB: 6OPD
Type: protein
Length: 384 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; Melanoma…
UniProt: P01892, P61769
Ligands: MG
Pockets: 4 · best druggability 0.71

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	Melanoma antigen variant	protein	9	0% helix, 0% strand	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B
GOL · Glycerol · additive · 4 copies · chains A, B, C
ACT · Acetate ion · additive · 3 copies · chains A, B

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

Pockets

4 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	708	0.71	0.78	60	GOL, MG
2	189	0.55	0.79	32	ACT, GOL
3	96	0.42	0.78	16	empty
4	83	0.36	0.76	18	ACT

Interfaces

2 interfaces between chains.

A–B · 1437 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 865 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6OPD · Crystal Structure of ILNAMIVKI peptide bound to 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

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 6OPD · PDBe 6OPD · UniProt P01892 · UniProt P61769

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