Research workbench

Structure of the human MHC I peptide-loading complex editing module

Analyse Structure of the human MHC I peptide-loading complex editing module in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7QPD
Type: protein
Length: 1,544 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-2-microglobulin; Tapasin; Protein disulfide-isomerase A3; HLA class I…
EC: 5.3.4.1
UniProt: P61769, O15533, P30101, P04439, P27797
Ligands: NAG, MAN, BMA, GLC
Pockets: 19 · best druggability 0.76

Structure

electron microscopy · 5 distinct chains · 20% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Beta-2-microglobulin	protein	99	0% helix, 39% strand	P61769
T	Tapasin	protein	348	6% helix, 37% strand	O15533
E	Protein disulfide-isomerase A3 (EC 5.3.4.1)	protein	459	35% helix, 18% strand	P30101
M	HLA class I histocompatibility antigen, a-3 alpha chain	protein	274	25% helix, 39% strand	P04439
C	Calreticulin	protein	364	17% helix, 30% strand	P27797

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains T, E, M, C
MAN · alpha-D-mannopyranose · sugar · 3 copies · chains T, C
BMA · beta-D-mannopyranose · sugar · 2 copies · chains C
GLC · alpha-D-glucopyranose · sugar · chains C

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

Pockets

19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1028	0.76	0.78	85	empty
2	80	0.72	0.96	28	empty
3	300	0.62	0.79	40	empty
4	87	0.61	0.89	24	empty
5	392	0.60	0.76	44	empty

Interfaces

8 interfaces between chains.

T–M · 1601 Å² buried · 15 hydrogen bonds · protein-protein
B–M · 1410 Å² buried · 11 hydrogen bonds · protein-protein
T–E · 1233 Å² buried · 10 hydrogen bonds · protein-protein
B–T · 539 Å² buried · 1 hydrogen bond · protein-protein
E–C · 413 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

7QPD · Structure of the human MHC I peptide-loading complex editing module · the same entry in another collection · chain C against C, 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 0.97
P04439 · AlphaFold monomer V2.0 prediction for HLA class I histocompatibility antigen, a alpha… · a predicted model of the same protein · chain M against A, TM-score 0.95
P30101 · AlphaFold monomer V2.0 prediction for protein disulfide-isomerase A3 (P30101) · a predicted model of the same protein · chain E against A, TM-score 0.94
P27797 · AlphaFold monomer V2.0 prediction for calreticulin (P27797) · a predicted model of the same protein · chain C against A, TM-score 0.93
O15533 · AlphaFold monomer V2.0 prediction for tapasin (O15533) · a predicted model of the same protein · chain T against A, TM-score 0.92

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 P61769
Every structure of UniProt O15533
Every structure of UniProt P30101
Every structure of UniProt P04439
Every structure of UniProt P27797
Elsewhere: RCSB PDB 7QPD · PDBe 7QPD · UniProt P61769 · UniProt O15533 · UniProt P30101 · UniProt P04439 · UniProt P27797

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