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Crystal structure of TK3 TCR-HLA-B*35:01-HPVG-Q5 complex

Analyse Crystal structure of TK3 TCR-HLA-B*35:01-HPVG-Q5 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4PRP
Type: protein
Length: 827 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.5
Source: Homo sapiens; SYNTHETIC CONSTRUCT
Molecule: MHC class I antigen; Beta-2-microglobulin; Epstein-Barr nuclear antigen 1; TK3 TCR alpha…
UniProt: C5MK56, P61769, P03211
Ligands: SO4
Pockets: 14 · best druggability 0.73

Structure

x-ray diffraction · resolution 2.5 · 5 distinct chains · 11% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen	protein	276	25% helix, 40% 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	200	3% helix, 48% strand	—
E	TK3 TCR beta chain	protein	241	6% helix, 51% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, B, E

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

Pockets

14 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	680	0.73	0.80	58	empty
2	1062	0.69	0.74	89	empty
3	116	0.51	0.81	27	empty
4	173	0.46	0.76	26	empty
5	189	0.46	0.75	29	empty

Interfaces

7 interfaces between chains.

D–E · 2128 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1273 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 918 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 418 Å² buried · 1 hydrogen bond · protein-protein
A–E · 304 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

4PRP · Crystal structure of TK3 TCR-HLA-B*35:01-hpvg-Q5 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 4PRP · PDBe 4PRP · UniProt C5MK56 · UniProt P61769 · UniProt P03211

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