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Crystal structure of TK3 TCR-HLA-B*35:08-hpvg complex

Analyse Crystal structure of TK3 TCR-HLA-B*35:08-hpvg complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4PRI
Type: protein
Length: 828 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; Epstein-barr nuclear antigen 1; TK3 TCR alpha…
UniProt: C5MK56, P61769, P03211
Ligands: NA, CL
Pockets: 10 · best druggability 0.71

Structure

x-ray diffraction · 5 distinct chains · 11% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen	protein	276	24% helix, 37% strand	C5MK56
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
C	Epstein-barr nuclear antigen 1	protein	11	0% helix, 0% strand	P03211
D	TK3 TCR alpha chain	protein	202	3% helix, 48% strand	—
E	TK3 TCR beta chain	protein	240	8% helix, 51% strand	—

Ligands and binding sites

NA · Sodium ion · metal · 3 copies · chains B, D, E
CL · Chloride ion · ion · 2 copies · chains A, D, E

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

Pockets

10 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	934	0.71	0.76	71	empty
2	539	0.69	0.79	52	empty
3	272	0.55	0.77	46	CL
4	185	0.49	0.76	23	empty
5	118	0.42	0.76	25	empty

Interfaces

7 interfaces between chains.

D–E · 2054 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1320 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 918 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 498 Å² buried · 1 hydrogen bond · protein-protein
A–E · 318 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4PRI · Crystal structure of TK3 TCR-HLA-B*35:08-HPVG complex · 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 C5MK56
Every structure of UniProt P61769
Every structure of UniProt P03211
Elsewhere: RCSB PDB 4PRI · PDBe 4PRI · UniProt C5MK56 · UniProt P61769 · UniProt P03211

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