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Crystal structure of EM2 TCR in complex with HLA-B*37:01-NP338

Analyse Crystal structure of EM2 TCR in complex with HLA-B*37:01-NP338 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MTM
Type: protein
Length: 814 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, B-37 alpha chain; Beta-2-microglobulin; NP338…
UniProt: P18463, P61769
Pockets: 9 · best druggability 0.73

Structure

x-ray diffraction · 5 distinct chains · 11% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, B-37 alpha chain	protein	276	26% helix, 39% strand	P18463
B	Beta-2-microglobulin	protein	99	0% helix, 46% strand	P61769
C	NP338 influenza peptide	protein	9	0% helix, 0% strand	—
D	EM2 TCR alpha chain	protein	193	2% helix, 41% strand	—
E	EM2 TCR beta chain	protein	237	6% helix, 51% strand	—

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	959	0.73	0.77	69	empty
2	681	0.70	0.78	56	empty
3	279	0.56	0.77	40	empty
4	156	0.50	0.78	26	empty
5	142	0.47	0.78	27	empty

Interfaces

7 interfaces between chains.

D–E · 2252 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1393 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 974 Å² buried · 19 hydrogen bonds · protein-protein
A–E · 540 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 318 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6MTM · Crystal Structure of EM2 TCR in complex with HLA-B*37:01-NP338 · the same entry in another collection · chain A against A, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P18463
Every structure of UniProt P61769
Elsewhere: RCSB PDB 6MTM · PDBe 6MTM · UniProt P18463 · UniProt P61769

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