MolNFT v1 · #179141 · protein

Crystal structure of B17-C1 TCR-H2DB

7JWJ · H-2 class I histocompatibility antigen, D-B alpha chain: “Crystal structure of B17-C1 TCR-H2DB”. X-ray diffraction, 10 pockets (best druggability 0.71). MolNFT v1 #179141 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7JWJ
Type: protein
Length: 811 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…
UniProt: P01899, P01887, Q9Q0U8
Pockets: 10 · best druggability 0.71

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	266	27% helix, 35% strand	P01899
B	Beta-2-microglobulin	protein	97	0% helix, 48% strand	P01887
C	Nucleoprotein	protein	9	0% helix, 0% strand	Q9Q0U8
D	B17.C1 TCR alpha chain	protein	196	2% helix, 45% strand	—
E	B17.C1 TCR alpha chain	protein	243	6% helix, 48% 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	851	0.71	0.76	76	empty
2	733	0.69	0.76	53	empty
3	361	0.68	0.82	53	empty
4	208	0.50	0.76	33	empty
5	76	0.48	0.83	19	empty

Interfaces

7 interfaces between chains.

D–E · 2379 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 1240 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 903 Å² buried · 23 hydrogen bonds · protein-protein
A–E · 436 Å² buried · 0 hydrogen bonds · protein-protein
C–E · 317 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

7JWJ · Crystal Structure of B17-C1 TCR-H2Db · 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 0.96

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
Every structure of UniProt Q9Q0U8
Elsewhere: RCSB PDB 7JWJ · PDBe 7JWJ · UniProt P01899 · UniProt P01887 · UniProt Q9Q0U8

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