MolNFT v1 · #185008 · protein

Emergence of immune escape at dominant SARS-cov-2 killer T-cell epitope

7PBE · MHC class I antigen: “Emergence of immune escape at dominant SARS-cov-2 killer T-cell epitope”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.77). MolNFT v1 #185008 on GenesisL1: 3D structure, binding sites and…

PDB: 7PBE
Type: protein
Length: 1,652 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; Spike protein S1; Human T-cell receptor YLQ36…
UniProt: A0A5B8RNS7, P61769, P0DTC2
Ligands: SO4
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 5 distinct chains · 10% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	MHC class I antigen	protein	276	23% helix, 38% strand	A0A5B8RNS7
B, G	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, H	Spike protein S1	protein	9	0% helix, 0% strand	P0DTC2
D, I	Human T-cell receptor YLQ36, alpha chain	protein	199	2% helix, 43% strand	—
E, J	Human T-cell receptor YLQ36, beta chain	protein	242	6% helix, 49% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, B, E, F, I
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, F

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

Pockets

20 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	936	0.77	0.80	74	empty
2	804	0.72	0.77	59	empty
3	640	0.68	0.77	54	empty
4	624	0.68	0.77	56	empty
5	141	0.58	0.83	22	empty

Interfaces

14 interfaces between chains.

D–E · 2395 Å² buried · 25 hydrogen bonds · protein-protein
I–J · 2383 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1474 Å² buried · 22 hydrogen bonds · protein-protein
F–G · 1468 Å² buried · 19 hydrogen bonds · protein-protein
F–H · 904 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

7PBE · Emergence of immune escape at dominant SARS-CoV-2 killer T-cell epitope · the same entry in another collection · chain J against J, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain G 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 A0A5B8RNS7
Every structure of UniProt P61769
Every structure of UniProt P0DTC2
Elsewhere: RCSB PDB 7PBE · PDBe 7PBE · UniProt A0A5B8RNS7 · UniProt P61769 · UniProt P0DTC2

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