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Crystal structure of TCR PF8 in complex with flu MP(58-66) epitope presented by HLA-A2

Analyse Crystal structure of TCR PF8 in complex with flu MP(58-66) epitope presented by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5E6I
Type: protein
Length: 3,204 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TCR alpha CHAIN,HUMAN nkt TCR alpha chain; T-cell receptor beta-2 chain C region; HLA…
UniProt: K7N5M3, A0A087WZ08, P01892, P61769, E9P5U1
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 17 distinct chains · 11% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	TCR alpha CHAIN,HUMAN nkt TCR alpha chain	protein	201	3% helix, 42% strand	K7N5M3
H	T-cell receptor beta-2 chain C region	protein	239	7% helix, 38% strand	A0A087WZ08
I	HLA class I histocompatibility antigen, a-2 alpha chain	protein	261	25% helix, 31% strand	P01892
J	Beta-2-microglobulin	protein	96	0% helix, 33% strand	P61769
K, E, O, T	Matrix protein 1	protein	9	0% helix, 0% strand	E9P5U1
A	TCR alpha CHAIN,HUMAN nkt TCR alpha chain	protein	196	2% helix, 43% strand	K7N5M3
B	T-cell receptor beta-2 chain C region	protein	241	6% helix, 40% strand	A0A087WZ08
C	HLA class I histocompatibility antigen, a-2 alpha chain	protein	258	27% helix, 29% strand	P01892
D	Beta-2-microglobulin	protein	97	0% helix, 42% strand	P61769
F	TCR alpha CHAIN,HUMAN nkt TCR alpha chain	protein	198	5% helix, 41% strand	K7N5M3
L	T-cell receptor beta-2 chain C region	protein	242	6% helix, 39% strand	A0A087WZ08
M	HLA class I histocompatibility antigen, a-2 alpha chain	protein	268	22% helix, 29% strand	P01892
N	Beta-2-microglobulin	protein	92	0% helix, 37% strand	P61769
P	TCR alpha CHAIN,HUMAN nkt TCR alpha chain	protein	191	2% helix, 40% strand	K7N5M3
Q	T-cell receptor beta-2 chain C region	protein	238	6% helix, 42% strand	A0A087WZ08
R	HLA class I histocompatibility antigen, a-2 alpha chain	protein	251	25% helix, 29% strand	P01892
U	Beta-2-microglobulin	protein	99	0% helix, 54% strand	P61769

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	1106	0.76	0.78	116	empty
2	1007	0.73	0.76	110	empty
3	1048	0.73	0.76	83	empty
4	605	0.71	0.80	64	empty
5	718	0.70	0.77	64	empty

Interfaces

41 interfaces between chains.

G–H · 2073 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 1974 Å² buried · 21 hydrogen bonds · protein-protein
P–Q · 1951 Å² buried · 15 hydrogen bonds · protein-protein
F–L · 1936 Å² buried · 23 hydrogen bonds · protein-protein
R–U · 1190 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 disulfide (disulfide).

Compared structures

5E6I · Crystal structure of TCR PF8 in complex with flu MP(58-66) epitope presented by HLA-A2 · the same entry in another collection · chain T against T, 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 K7N5M3
Every structure of UniProt A0A087WZ08
Every structure of UniProt P01892
Every structure of UniProt P61769
Every structure of UniProt E9P5U1
Elsewhere: RCSB PDB 5E6I · PDBe 5E6I · UniProt K7N5M3 · UniProt A0A087WZ08 · UniProt P01892 · UniProt P61769 · UniProt E9P5U1

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