MolNFT v2 · #225721 · protein
The complex of TCR NYN-I and HLA-A24 bound to SARS-CoV-2 Spike448-456 peptide NYNYLYRLF
8YE4 · MHC class I antigen precusor: “The complex of TCR NYN-I and HLA-A24 bound to SARS-CoV-2 Spike448-456 peptide NYNYLYRLF”. X-ray diffraction at 3.2, 20 pockets (best druggability 0.77). MolNFT v2 #225721 on GenesisL1: 3D structure…
- PDB
- 8YE4
- Type
- protein
- Length
- 1,554 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- MHC class I antigen precusor; Beta-2-microglobulin; Spike protein S1; TCR NYN-I alpha…
- UniProt
- Q6IVJ7, P61769, P0DTC2
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · resolution 3.2 · 8 distinct chains · 13% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen precusor | protein | 274 | 27% helix, 36% strand | Q6IVJ7 |
| B, D | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| E, F | Spike protein S1 | protein | 9 | 0% helix, 0% strand | P0DTC2 |
| C | MHC class I antigen precusor | protein | 233 | 30% helix, 29% strand | Q6IVJ7 |
| G | TCR NYN-I alpha chain | protein | 183 | 3% helix, 42% strand | — |
| H | TCR NYN-I beta chain | protein | 238 | 8% helix, 48% strand | — |
| I | TCR NYN-I alpha chain | protein | 178 | 3% helix, 46% strand | — |
| J | TCR NYN-I beta chain | protein | 232 | 6% helix, 49% strand | — |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 715 | 0.77 | 0.82 | 87 | empty |
| 2 | 1089 | 0.74 | 0.77 | 87 | empty |
| 3 | 1041 | 0.73 | 0.76 | 79 | empty |
| 4 | 615 | 0.69 | 0.78 | 52 | empty |
| 5 | 573 | 0.68 | 0.78 | 59 | empty |
Interfaces
19 interfaces between chains.
- G–H · 2003 Ų buried · 23 hydrogen bonds · protein-protein
- I–J · 1786 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1379 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1303 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 1034 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain D 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 Q6IVJ7
- Every structure of UniProt P61769
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 8YE4 · PDBe 8YE4 · UniProt Q6IVJ7 · UniProt P61769 · UniProt P0DTC2
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