Research workbench
Single chain trimer HLA-A*02:01 (H98L, Y108C) with HPV.16 E7 peptide YMLDLQPETTDL
Analyse Single chain trimer HLA-A*02:01 (H98L, Y108C) with HPV.16 E7 peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SR3
- Type
- protein
- Length
- 933 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.49
- Source
- Homo sapiens; Human papillomavirus type 16; Lama glama; Pongo pygmaeus
- Molecule
- Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera; Vhh
- UniProt
- P03129, P16213, A0A678ZGP6
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · resolution 2.49 · 4 distinct chains · 17% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera | protein | 356 | 21% helix, 38% strand | P03129, P16213, A0A678ZGP6 |
| B | Vhh | protein | 112 | 5% helix, 49% strand | — |
| C | Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera | protein | 352 | 20% helix, 39% strand | P03129, P16213, A0A678ZGP6 |
| D | Vhh | protein | 113 | 8% helix, 50% strand | — |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.65 | 0.76 | 53 | empty |
| 2 | 484 | 0.65 | 0.77 | 45 | empty |
| 3 | 354 | 0.57 | 0.76 | 49 | empty |
| 4 | 318 | 0.55 | 0.75 | 46 | empty |
| 5 | 197 | 0.52 | 0.77 | 30 | empty |
Interfaces
3 interfaces between chains.
- C–D · 917 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 879 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 191 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- P16213 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P16213) · a predicted model of the same protein · chain C against A, TM-score 0.28
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 P03129
- Every structure of UniProt P16213
- Every structure of UniProt A0A678ZGP6
- Elsewhere: RCSB PDB 7SR3 · PDBe 7SR3 · UniProt P03129 · UniProt P16213 · UniProt A0A678ZGP6
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