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Crystal structure of 3A6 TCR bound to MBP/HLA-DR2A

Analyse Crystal structure of 3A6 TCR bound to MBP/HLA-DR2A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1ZGL
Type: protein
Length: 3,150 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class II histocompatibility antigen, dr alpha chain; Major histocompatibility…
UniProt: P01903, Q29787, Q6AI64, P01848, P01850
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 16 distinct chains · 8% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, G, J	HLA class II histocompatibility antigen, dr alpha chain	protein	178	12% helix, 44% strand	P01903
B	Major histocompatibility complex, class II, dr beta 5	protein	175	19% helix, 36% strand	Q29787
C, L	Myelin basic protein	protein	14	0% helix, 14% strand	Q6AI64
M	T cell receptor alpha chain	protein	178	3% helix, 28% strand	P01848
P	T cell receptor beta chain	protein	242	4% helix, 38% strand	P01850
E	Major histocompatibility complex, class II, dr beta 5	protein	175	17% helix, 37% strand	Q29787
F	Myelin basic protein	protein	15	0% helix, 7% strand	Q6AI64
Q	T cell receptor alpha chain	protein	187	2% helix, 30% strand	P01848
R	T cell receptor beta chain	protein	238	5% helix, 37% strand	P01850
H	Major histocompatibility complex, class II, dr beta 5	protein	168	20% helix, 39% strand	Q29787
I	Myelin basic protein	protein	13	0% helix, 0% strand	Q6AI64
S	T cell receptor alpha chain	protein	176	2% helix, 23% strand	P01848
T	T cell receptor beta chain	protein	226	3% helix, 30% strand	P01850
K	Major histocompatibility complex, class II, dr beta 5	protein	180	17% helix, 41% strand	Q29787
U	T cell receptor alpha chain	protein	195	3% helix, 29% strand	P01848
V	T cell receptor beta chain	protein	242	5% helix, 43% strand	P01850

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	987	0.87	0.89	145	empty
2	873	0.85	0.87	121	empty
3	91	0.75	0.97	29	empty
4	100	0.75	0.96	30	empty
5	769	0.75	0.79	78	empty

Interfaces

74 interfaces between chains.

D–E · 2480 Å² buried · 38 hydrogen bonds · protein-protein
J–K · 2454 Å² buried · 42 hydrogen bonds · protein-protein
G–H · 2404 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 2360 Å² buried · 34 hydrogen bonds · protein-protein
U–V · 1917 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 26 disulfide (disulfide).

Compared structures

1ZGL · Crystal structure of 3A6 TCR bound to MBP/HLA-DR2a · the same entry in another collection · chain R against R, 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 Q29787
Every structure of UniProt Q6AI64
Every structure of UniProt P01848
Every structure of UniProt P01850
Elsewhere: RCSB PDB 1ZGL · PDBe 1ZGL · UniProt P01903 · UniProt Q29787 · UniProt Q6AI64 · UniProt P01848 · UniProt P01850

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