MolNFT v1 · #104898 · protein

Structural basis for ineffective T-cell responses to MHC anchor residue improved heteroclitic peptides

4QOK · HLA class I histocompatibility antigen, a-2 alpha chain: “Structural basis for ineffective T-cell responses to MHC anchor residue improved heteroclitic peptides”. X-ray diffraction, 12 pockets (best druggability 0.71). MolNFT v1…

PDB: 4QOK
Type: protein
Length: 824 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin; Melanoma…
UniProt: P01892, P61769, Q16655
Pockets: 12 · best druggability 0.71

Structure

x-ray diffraction · 5 distinct chains · 11% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, a-2 alpha chain	protein	276	25% helix, 37% strand	P01892
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	Melanoma antigen recognized by T-cells 1 marker peptide	protein	10	0% helix, 10% strand	Q16655
D	MEL5 TCR chain alpha	protein	194	2% helix, 44% strand	—
E	MEL5 TCR chain beta	protein	244	6% helix, 50% strand	—

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, D, E

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

Pockets

12 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	979	0.71	0.75	76	EDO
2	652	0.68	0.77	61	empty
3	372	0.66	0.80	47	empty
4	186	0.50	0.77	35	empty
5	105	0.46	0.80	31	empty

Interfaces

7 interfaces between chains.

D–E · 2131 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1408 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 846 Å² buried · 15 hydrogen bonds · protein-protein
A–E · 497 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 481 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4QOK · Structural basis for ineffective T-cell responses to MHC anchor residue improved… · the same entry in another collection · chain B against B, 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
Q16655 · AlphaFold monomer V2.0 prediction for melanoma antigen recognized by T-cells 1 (Q16655) · a predicted model of the same protein · chain C against A, TM-score 0.25

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 P01892
Every structure of UniProt P61769
Every structure of UniProt Q16655
Elsewhere: RCSB PDB 4QOK · PDBe 4QOK · UniProt P01892 · UniProt P61769 · UniProt Q16655

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