MolNFT v1 · #40009 · protein

Crystal structure of a complete ternary complex between TCR, superantigen, and peptide-MHC class II molecule

2ICW · HLA class II histocompatibility antigen, dr alpha chain: “Crystal structure of a complete ternary complex between TCR, superantigen, and peptide-MHC class II molecule”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT…

PDB: 2ICW
Type: protein
Length: 1,622 residues
Chains: 12
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, P04229, Q48898, P01738, P04213
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 9 distinct chains · 21% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	HLA class II histocompatibility antigen, dr alpha chain	protein	179	13% helix, 46% strand	P01903
B	HLA class II histocompatibility antigen, DRB1-1 beta chain	protein	184	19% helix, 42% strand	P04229
C, F	Haemagglutinin peptide	protein	13	0% helix, 8% strand	—
E	HLA class II histocompatibility antigen, DRB1-1 beta chain	protein	185	19% helix, 42% strand	P04229
G, H	Mycoplasma arthritidis mitogen	protein	213	69% helix, 0% strand	Q48898
I	T-cell receptor alpha chain V	protein	110	3% helix, 46% strand	P01738
J	T-cell receptor beta chain V	protein	113	3% helix, 48% strand	P04213
K	T-cell receptor alpha chain V	protein	109	3% helix, 47% strand	P01738
L	T-cell receptor beta chain V	protein	111	3% helix, 49% strand	P04213

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1167	0.83	0.84	109	empty
2	587	0.80	0.86	60	empty
3	447	0.68	0.79	51	empty
4	164	0.65	0.86	33	empty
5	55	0.61	0.92	19	empty

Interfaces

27 interfaces between chains.

A–B · 2559 Å² buried · 43 hydrogen bonds · protein-protein
D–E · 2531 Å² buried · 43 hydrogen bonds · protein-protein
G–J · 1139 Å² buried · 22 hydrogen bonds · protein-protein
H–L · 1110 Å² buried · 20 hydrogen bonds · protein-protein
A–G · 767 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 6 modified (disulfide, engineered).

Compared structures

2ICW · Crystal structure of a complete ternary complex between TCR, superantigen, and… · the same entry in another collection · chain L against L, TM-score 1.00

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 P04229
Every structure of UniProt Q48898
Every structure of UniProt P01738
Every structure of UniProt P04213
Elsewhere: RCSB PDB 2ICW · PDBe 2ICW · UniProt P01903 · UniProt P04229 · UniProt Q48898 · UniProt P01738 · UniProt P04213

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