MolNFT v1 · #13092 · protein
T cell receptor beta chain complexed with superantigen spea soaked with zinc
1L0Y · 14.3.D T cell receptor beta chain: “T cell receptor beta chain complexed with superantigen spea soaked with zinc”. X-ray diffraction, 1 ligand (ZN), 11 pockets (best druggability 0.70). MolNFT v1 #13092 on GenesisL1: 3D structure…
- PDB
- 1L0Y
- Type
- protein
- Length
- 913 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 14.3.D T cell receptor beta chain; Exotoxin type a
- UniProt
- P01851, P08095
- Ligands
- ZN
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 14.3.D T cell receptor beta chain | protein | 236 | 7% helix, 52% strand | P01851 |
| B | Exotoxin type a | protein | 220 | 20% helix, 38% strand | P08095 |
| D | Exotoxin type a | protein | 221 | 20% helix, 39% strand | P08095 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.70 | 0.77 | 66 | empty |
| 2 | 706 | 0.66 | 0.75 | 49 | empty |
| 3 | 490 | 0.65 | 0.77 | 48 | empty |
| 4 | 145 | 0.56 | 0.82 | 23 | empty |
| 5 | 212 | 0.52 | 0.77 | 30 | empty |
Interfaces
5 interfaces between chains.
- A–B · 616 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 613 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 589 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 214 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 94 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1L0Y · T cell receptor beta chain complexed with superantigen SpeA soaked with zinc · the same entry in another collection · chain A against A, TM-score 1.00
- P01851 · AlphaFold monomer V2.0 prediction for T-cell receptor beta-2 chain C region (P01851) · a predicted model of the same protein · chain A against A, TM-score 0.52
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 P01851
- Every structure of UniProt P08095
- Elsewhere: RCSB PDB 1L0Y · PDBe 1L0Y · UniProt P01851 · UniProt P08095
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