Research workbench

6218 TCR in complex with H2-db PA224-233 with a cysteine mutant

Analyse 6218 TCR in complex with H2-db PA224-233 with a cysteine mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7N5P
Type: protein
Length: 815 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; Peptide…
UniProt: P01899, P61769, O89752, A0A075B6C4, K7N5N2, A0A0G2LB96, K7N5M4
Ligands: NA
Pockets: 13 · best druggability 0.68

Structure

x-ray diffraction · 5 distinct chains · 11% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, D-B alpha chain	protein	272	26% helix, 39% strand	P01899
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	Peptide from polymerase acidic protein	protein	10	0% helix, 0% strand	O89752
D	Fusion protein of T cell receptor alpha variable 21-DV12 and T-cell receptor, SP3.4 alpha chain	protein	198	2% helix, 43% strand	A0A075B6C4, K7N5N2
E	Fusion protein of T cell receptor beta, variable 29 and human nkt TCR beta chain	protein	235	6% helix, 51% strand	A0A0G2LB96, K7N5M4

Ligands and binding sites

NA · Sodium ion · metal · 4 copies · chains D, A, E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	722	0.68	0.76	51	NA
2	512	0.66	0.77	51	empty
3	252	0.54	0.77	40	empty
4	149	0.47	0.77	31	empty
5	120	0.41	0.76	19	empty

Interfaces

7 interfaces between chains.

D–E · 2136 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1370 Å² buried · 25 hydrogen bonds · protein-protein
A–C · 916 Å² buried · 30 hydrogen bonds · protein-protein
A–E · 406 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 299 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

7N5P · 6218 TCR in complex with H2-Db PA224-233 with a cysteine mutant · 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 P01899
Every structure of UniProt P61769
Every structure of UniProt O89752
Every structure of UniProt A0A075B6C4
Every structure of UniProt K7N5N2
Every structure of UniProt A0A0G2LB96
Every structure of UniProt K7N5M4
Elsewhere: RCSB PDB 7N5P · PDBe 7N5P · UniProt P01899 · UniProt P61769 · UniProt O89752 · UniProt A0A075B6C4 · UniProt K7N5N2 · UniProt A0A0G2LB96 · UniProt K7N5M4

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