MolNFT v1 · #103090 · protein

14.C6 TCR complexed with MHC class II I-AB/3K peptide

4P5T · Tra protein: “14.C6 TCR complexed with MHC class II I-AB/3K peptide”. X-ray diffraction, 17 pockets (best druggability 0.70). MolNFT v1 #103090 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4P5T
Type: protein
Length: 1,608 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tra protein; Human nkt TCR beta chain; H-2 class II histocompatibility antigen, a-B alpha…
UniProt: P14434, P14483
Pockets: 17 · best druggability 0.70

Structure

x-ray diffraction · 6 distinct chains · 8% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tra protein	protein	197	2% helix, 47% strand	—
B	Human nkt TCR beta chain	protein	238	6% helix, 51% strand	—
C, G	H-2 class II histocompatibility antigen, a-B alpha chain	protein	179	14% helix, 44% strand	P14434
D, H	Protein of 3K peptide (FEAQKAKANKAVD),LINKER region - GGGGSLVPRGSGGGG,H-2 class II histocompatibility antigen, a beta CHAIN,H-2 class II histocompatibility antigen, a beta chain	protein	199	18% helix, 43% strand	P14483
E	Tra protein	protein	188	2% helix, 49% strand	—
F	Human nkt TCR beta chain	protein	229	6% helix, 53% strand	—

Pockets

17 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	937	0.70	0.75	72	empty
2	905	0.69	0.75	66	empty
3	146	0.44	0.76	20	empty
4	139	0.44	0.76	22	empty
5	79	0.43	0.80	17	empty

Interfaces

12 interfaces between chains.

C–D · 2914 Å² buried · 51 hydrogen bonds · protein-protein
G–H · 2878 Å² buried · 54 hydrogen bonds · protein-protein
A–B · 2122 Å² buried · 37 hydrogen bonds · protein-protein
E–F · 1999 Å² buried · 31 hydrogen bonds · protein-protein
A–D · 451 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

4P5T · 14.C6 TCR complexed with MHC class II I-Ab/3K peptide · the same entry in another collection · chain H against H, TM-score 1.00
P14434 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a-B alpha… · a predicted model of the same protein · chain C against A, TM-score 0.95
P14483 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a beta… · a predicted model of the same protein · chain D against A, TM-score 0.71

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 P14434
Every structure of UniProt P14483
Elsewhere: RCSB PDB 4P5T · PDBe 4P5T · UniProt P14434 · UniProt P14483

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