MolNFT v1 · #154020 · protein

Structure of human T cell receptor-CD3 complex

6JXR · T-cell surface glycoprotein CD3 zeta chain: “Structure of human T cell receptor-CD3 complex”. Electron microscopy, 9 pockets (best druggability 0.84). MolNFT v1 #154020 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6JXR
Type: protein
Length: 1,073 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: T-cell surface glycoprotein CD3 zeta chain; T-cell surface glycoprotein CD3 delta chain…
UniProt: P20963, P04234, P07766, P09693, A0A0B4J271, A0N4Z6, P01848, A0A0K0K1A5, P0DSE2, A0A0G2JMB4
Pockets: 9 · best druggability 0.84

Structure

electron microscopy · 8 distinct chains · 24% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
a	T-cell surface glycoprotein CD3 zeta chain	protein	36	78% helix, 0% strand	P20963
b	T-cell surface glycoprotein CD3 zeta chain	protein	32	81% helix, 0% strand	P20963
d	T-cell surface glycoprotein CD3 delta chain	protein	108	25% helix, 35% strand	P04234
f	T-cell surface glycoprotein CD3 epsilon chain	protein	124	23% helix, 31% strand	P07766
g	T-cell surface glycoprotein CD3 gamma chain	protein	115	22% helix, 36% strand	P09693
m	T cell receptor alpha variable 12-3,POSSIBLE J 11 gene SEGMENT,T cell receptor alpha constant	protein	248	17% helix, 33% strand	A0A0B4J271, A0N4Z6, P01848
n	T cell receptor beta variable 6-5,M1-specific T cell receptor beta CHAIN,T cell receptor beta constant 2	protein	287	16% helix, 38% strand	A0A0K0K1A5, P0DSE2, A0A0G2JMB4
e	T-cell surface glycoprotein CD3 epsilon chain	protein	123	24% helix, 34% strand	P07766

Pockets

9 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	1018	0.84	0.85	90	empty
2	704	0.82	0.86	85	empty
3	1137	0.73	0.76	90	empty
4	521	0.72	0.81	58	empty
5	515	0.67	0.78	40	empty

Interfaces

22 interfaces between chains.

m–n · 3854 Å² buried · 30 hydrogen bonds · protein-protein
f–g · 1700 Å² buried · 20 hydrogen bonds · protein-protein
d–e · 1678 Å² buried · 23 hydrogen bonds · protein-protein
d–m · 1210 Å² buried · 13 hydrogen bonds · protein-protein
g–n · 841 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

6JXR · Structure of human T cell receptor-CD3 complex · the same entry in another collection · chain e against e, TM-score 1.00
P0DSE2 · AlphaFold monomer V2.0 prediction for M1-specific T cell receptor beta chain (P0DSE2) · a predicted model of the same protein · chain n against A, TM-score 0.96
P07766 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD3 epsilon chain… · a predicted model of the same protein · chain f against A, TM-score 0.88
P20963 · P20963 · a predicted model of the same protein · chain b against A, TM-score 0.78

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 P20963
Every structure of UniProt P04234
Every structure of UniProt P07766
Every structure of UniProt P09693
Every structure of UniProt A0A0B4J271
Every structure of UniProt A0N4Z6
Every structure of UniProt P01848
Every structure of UniProt A0A0K0K1A5
Every structure of UniProt P0DSE2
Every structure of UniProt A0A0G2JMB4
Elsewhere: RCSB PDB 6JXR · PDBe 6JXR · UniProt P20963 · UniProt P04234 · UniProt P07766 · UniProt P09693 · UniProt A0A0B4J271 · UniProt A0N4Z6 · UniProt P01848 · UniProt A0A0K0K1A5 · UniProt P0DSE2 · UniProt A0A0G2JMB4

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