Research workbench

Crystal structure of the tapbpr-MHC I peptide editing complex

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

PDB: 5OPI
Type: protein
Length: 709 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class I histocompatibility antigen, D-B alpha chain; Beta-2-microglobulin; Tap…
UniProt: P01899, P61769, Q53GH5
Pockets: 8 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 13% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, D-B alpha chain	protein	278	27% helix, 41% strand	P01899
B	Beta-2-microglobulin	protein	99	0% helix, 60% strand	P61769
C	Tap binding protein-like variant	protein	332	5% helix, 44% strand	Q53GH5

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1005	0.76	0.79	93	empty
2	181	0.73	0.89	34	empty
3	227	0.70	0.86	38	empty
4	666	0.67	0.76	63	empty
5	212	0.56	0.79	31	empty

Interfaces

3 interfaces between chains.

A–C · 1675 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 1282 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 605 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

5OPI · Crystal structure of the TAPBPR-MHC I peptide editing complex · 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 0.95

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 P01899
Every structure of UniProt P61769
Every structure of UniProt Q53GH5
Elsewhere: RCSB PDB 5OPI · PDBe 5OPI · UniProt P01899 · UniProt P61769 · UniProt Q53GH5

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