Research workbench

Crystal structure of HLA-A*1101 with SARS nucleocapsid peptide

Analyse Crystal structure of HLA-A*1101 with SARS nucleocapsid peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1X7Q
Type: protein
Length: 383 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, a-11 alpha chain; Beta-2-microglobulin; SARS…
UniProt: P13746, P61769, P59595
Ligands: SO4
Pockets: 4 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, a-11 alpha chain	protein	275	26% helix, 40% strand	P13746
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
C	SARS nucleocapsid peptide	protein	9	0% helix, 0% strand	P59595

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, C, B
GOL · Glycerol · additive · 7 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	655	0.68	0.77	61	GOL
2	94	0.47	0.81	21	empty
3	122	0.44	0.77	22	empty
4	61	0.30	0.75	15	empty

Interfaces

2 interfaces between chains.

A–B · 1265 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 933 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

1X7Q · Crystal structure of HLA-A*1101 with sars nucleocapsid peptide · 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 0.99

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 P13746
Every structure of UniProt P61769
Every structure of UniProt P59595
Elsewhere: RCSB PDB 1X7Q · PDBe 1X7Q · UniProt P13746 · UniProt P61769 · UniProt P59595

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