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Crystal structure of HLA A*1101 in complex with salewiknk, an 9-mer epitope from influenza B

Analyse Crystal structure of HLA A*1101 in complex with salewiknk, an 9-mer epitope… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7S8R
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 alpha chain; Beta-2-microglobulin; Matrix…
UniProt: U5YJK1, P61769, P13879
Ligands: MG, SO4
Pockets: 9 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	HLA class I histocompatibility antigen, a alpha chain	protein	275	23% helix, 40% strand	U5YJK1
B, E	Beta-2-microglobulin	protein	100	0% helix, 51% strand	P61769
C, F	Matrix protein 1 peptide salewiknk	protein	9	0% helix, 0% strand	P13879

Ligands and binding sites

MG · Magnesium ion · metal · 3 copies · chains A, B, D, E
SO4 · Sulfate ion · ion · 2 copies · chains B, D

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

Pockets

9 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	931	0.74	0.77	66	empty
2	1106	0.71	0.75	88	MG, SO4
3	750	0.70	0.77	60	MG
4	627	0.68	0.77	57	MG
5	168	0.44	0.75	24	empty

Interfaces

8 interfaces between chains.

D–E · 1424 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1393 Å² buried · 23 hydrogen bonds · protein-protein
D–F · 952 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 908 Å² buried · 19 hydrogen bonds · protein-protein
B–E · 400 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

7S8R · Crystal Structure of HLA A*1101 in complex with SALEWIKNK, an 9-mer epitope from… · 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 U5YJK1
Every structure of UniProt P61769
Every structure of UniProt P13879
Elsewhere: RCSB PDB 7S8R · PDBe 7S8R · UniProt U5YJK1 · UniProt P61769 · UniProt P13879

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