Research workbench

Crystal structure of NP2-B17 TCR-H2DB-np complex

Analyse Crystal structure of NP2-B17 TCR-H2DB-np complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5SWS
Type: protein
Length: 816 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class I histocompatibility antigen, D-B alpha chain; Beta-2-microglobulin; Influenza…
UniProt: P01899, P01887
Pockets: 10 · best druggability 0.72

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, D-B alpha chain	protein	273	26% helix, 37% strand	P01899
B	Beta-2-microglobulin	protein	97	0% helix, 48% strand	P01887
C	Influenza NP366 epitope	protein	9	0% helix, 0% strand	—
D	NP1-B17 TCR alpha chain	protein	198	2% helix, 42% strand	—
E	NP1-B17 TCR beta chain	protein	239	6% helix, 49% strand	—

Pockets

10 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	974	0.72	0.76	70	empty
2	726	0.70	0.77	59	empty
3	307	0.58	0.77	41	empty
4	71	0.57	0.88	22	empty
5	108	0.41	0.76	28	empty

Interfaces

6 interfaces between chains.

D–E · 2164 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1248 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 913 Å² buried · 29 hydrogen bonds · protein-protein
A–E · 626 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 353 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

5SWS · Crystal Structure of NP2-B17 TCR-H2Db-NP complex · the same entry in another collection · chain A against A, TM-score 1.00
P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · 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 P01899
Every structure of UniProt P01887
Elsewhere: RCSB PDB 5SWS · PDBe 5SWS · UniProt P01899 · UniProt P01887

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