Research workbench
MHC I A02 Allele presenting YLQPRTFLL
Analyse MHC I A02 Allele presenting YLQPRTFLL in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P3D
- Type
- protein
- Length
- 385 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.67
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Spike glycoprotein
- UniProt
- A0A5B8RNS7, P61769, P0DTC2
- Ligands
- CA
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · resolution 1.67 · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 276 | 27% helix, 40% strand | A0A5B8RNS7 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Spike glycoprotein | protein | 9 | 0% helix, 0% strand | P0DTC2 |
Ligands and binding sites
- CA · Calcium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, C, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.69 | 0.77 | 55 | EDO |
| 2 | 99 | 0.46 | 0.80 | 19 | EDO |
| 3 | 76 | 0.42 | 0.80 | 17 | EDO |
| 4 | 56 | 0.33 | 0.77 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1362 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 862 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
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 A0A5B8RNS7
- Every structure of UniProt P61769
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7P3D · PDBe 7P3D · UniProt A0A5B8RNS7 · UniProt P61769 · UniProt P0DTC2
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