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Crystal structure of the TK3 TCR in complex with HLA-B*3501/HPVG

Analyse Crystal structure of the TK3 TCR in complex with HLA-B*3501/HPVG in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3MV7
Type: protein
Length: 827 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, B-35 alpha chain; Beta-2-microglobulin; Hpvg…
UniProt: P30685, P61769, P03211
Ligands: SO4
Pockets: 10 · best druggability 0.69

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, B-35 alpha chain	protein	276	25% helix, 39% strand	P30685
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
C	Hpvg peptide from epstein-barr nuclear antigen 1	protein	11	0% helix, 0% strand	P03211
D	Alpha chain of the TK3 TCR	protein	200	5% helix, 48% strand	—
E	Beta chain of the TK3 TCR	protein	241	6% helix, 51% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · chains 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	1047	0.69	0.74	78	empty
2	617	0.69	0.77	56	empty
3	190	0.53	0.78	35	empty
4	131	0.48	0.79	30	empty
5	180	0.46	0.76	29	empty

Interfaces

7 interfaces between chains.

D–E · 2212 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1208 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 909 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 401 Å² buried · 1 hydrogen bond · protein-protein
A–E · 293 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

3MV7 · Crystal Structure of the TK3 TCR in complex with HLA-B*3501/HPVG · the same entry in another collection · chain E against E, 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 P30685
Every structure of UniProt P61769
Every structure of UniProt P03211
Elsewhere: RCSB PDB 3MV7 · PDBe 3MV7 · UniProt P30685 · UniProt P61769 · UniProt P03211

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