Research workbench

Structure of a fully assembled T-cell receptor engaging a tumor- associated peptide-MHC I

Analyse Structure of a fully assembled T-cell receptor engaging a tumor- associated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7PHR
Type: protein
Length: 1,443 residues
Chains: 11
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: T-cell receptor alpha chain; T-cell receptor beta chain; T-cell surface glycoprotein CD3…
UniProt: P09693, P04234, P07766, P04439, P61769, P40967, P20963
Ligands: NAG
Pockets: 14 · best druggability 0.83

Structure

electron microscopy · 11 distinct chains · 24% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	T-cell receptor alpha chain	protein	243	19% helix, 36% strand	—
B	T-cell receptor beta chain	protein	285	18% helix, 41% strand	—
C	T-cell surface glycoprotein CD3 gamma chain	protein	114	25% helix, 34% strand	P09693
D	T-cell surface glycoprotein CD3 delta chain, green fluorescent protein	protein	108	28% helix, 37% strand	P04234
E	T-cell surface glycoprotein CD3 epsilon chain	protein	123	24% helix, 34% strand	P07766
H	HLA class I histocompatibility antigen, a alpha chain	protein	275	25% helix, 39% strand	P04439
L	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
P	Tumor-associated antigentic peptide GP100	protein	9	0% helix, 0% strand	P40967
Z	T-cell surface glycoprotein CD3 zeta chain	protein	34	85% helix, 0% strand	P20963
e	T-cell surface glycoprotein CD3 epsilon chain	protein	124	26% helix, 31% strand	P07766
z	T-cell surface glycoprotein CD3 zeta chain	protein	29	93% helix, 0% strand	P20963

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, D

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

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1159	0.83	0.83	86	empty
2	684	0.81	0.86	91	empty
3	962	0.72	0.76	82	empty
4	450	0.72	0.82	51	empty
5	630	0.70	0.78	52	empty

Interfaces

27 interfaces between chains.

A–B · 3673 Å² buried · 40 hydrogen bonds · protein-protein
C–e · 1798 Å² buried · 25 hydrogen bonds · protein-protein
D–E · 1773 Å² buried · 26 hydrogen bonds · protein-protein
H–L · 1427 Å² buried · 19 hydrogen bonds · protein-protein
A–D · 1228 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 17 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

7PHR · Structure of a fully assembled T-cell receptor engaging a tumor-associated peptide-MHC I · the same entry in another collection · chain z against z, TM-score 1.00
P04439 · AlphaFold monomer V2.0 prediction for HLA class I histocompatibility antigen, a alpha… · a predicted model of the same protein · chain H against A, TM-score 0.99

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 P09693
Every structure of UniProt P04234
Every structure of UniProt P07766
Every structure of UniProt P04439
Every structure of UniProt P61769
Every structure of UniProt P40967
Every structure of UniProt P20963
Elsewhere: RCSB PDB 7PHR · PDBe 7PHR · UniProt P09693 · UniProt P04234 · UniProt P07766 · UniProt P04439 · UniProt P61769 · UniProt P40967 · UniProt P20963

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.