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Crystal structure of HLA-C*1402 complexed with 4-mer lipopeptide

Analyse Crystal structure of HLA-C*1402 complexed with 4-mer lipopeptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7WJ3
Type: protein
Length: 379 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I protein; Beta-2-microglobulin; 4-mer lipopeptide
UniProt: A0A890UPS4, P61769
Ligands: MYR
Pockets: 5 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I protein	protein	275	28% helix, 39% strand	A0A890UPS4
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	4-mer lipopeptide	protein	4	0% helix, 0% strand	—

Ligands and binding sites

MYR · Myristic acid · ligand · chains A, C
EDO · 1,2-ethanediol · additive · 18 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	671	0.71	0.78	57	EDO
2	289	0.68	0.83	36	EDO, MYR
3	196	0.53	0.78	39	EDO
4	81	0.39	0.78	16	empty
5	50	0.39	0.82	16	EDO

Interfaces

2 interfaces between chains.

A–B · 1374 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 345 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 1 lipid (disulfide, myristoylation).

Compared structures

7WJ3 · Crystal structure of HLA-C*1402 complexed with 4-mer lipopeptide · 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 A0A890UPS4
Every structure of UniProt P61769
Elsewhere: RCSB PDB 7WJ3 · PDBe 7WJ3 · UniProt A0A890UPS4 · UniProt P61769

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