Research workbench

Immune receptor complex

Analyse Immune receptor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6V0Y
Type: protein
Length: 812 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class II histocompatibility antigen, dr alpha chain; HLA class II histocompatibility…
UniProt: P01903, P13760
Ligands: CIR, NAG
Pockets: 13 · best druggability 0.74

Structure

x-ray diffraction · 5 distinct chains · 9% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class II histocompatibility antigen, dr alpha chain	protein	175	13% helix, 45% strand	P01903
B	HLA class II histocompatibility antigen, DRB1-4 beta chain	protein	179	15% helix, 42% strand	P13760
C	Fibrinogen beta 72,74CIT69-81	protein	11	0% helix, 0% strand	—
D	M141 TCR alpha chain	protein	205	1% helix, 44% strand	—
E	M141 TCR beta chain	protein	242	7% helix, 52% strand	—

Ligands and binding sites

CIR · Citrulline · ligand · 2 copies · chains A, B, C, D, E
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
GOL · Glycerol · additive · 4 copies · chains B, D, E

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

Pockets

13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	94	0.74	0.96	21	CIR
2	987	0.71	0.75	81	empty
3	65	0.46	0.83	17	empty
4	121	0.41	0.76	24	empty
5	94	0.39	0.77	15	empty

Interfaces

10 interfaces between chains.

A–B · 2341 Å² buried · 40 hydrogen bonds · protein-protein
D–E · 2229 Å² buried · 29 hydrogen bonds · protein-protein
A–C · 525 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 511 Å² buried · 5 hydrogen bonds · protein-protein
B–E · 383 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 4 covalent, 3 glycan (disulfide, covalent ligand, N-glycosylation).

Compared structures

6V0Y · immune receptor complex · the same entry in another collection · chain A against A, TM-score 1.00
P01903 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr alpha… · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P01903
Every structure of UniProt P13760
Elsewhere: RCSB PDB 6V0Y · PDBe 6V0Y · UniProt P01903 · UniProt P13760

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