Research workbench
Consequences of HLA single chain trimer mutations on peptide presentation and binding affinity
Analyse Consequences of HLA single chain trimer mutations on peptide presentation and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ST3
- Type
- protein
- Length
- 7,611 residues
- Chains
- 32
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.78
- 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
- 20 · best druggability 0.68
Structure
x-ray diffraction · resolution 2.78 · 17 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera | protein | 352 | 20% helix, 40% strand | P03129, P16213, A0A678ZGP6 |
| B, D, F, H, J, L, N, P, R, T, V, X, Z, b, d, f | Vhh | protein | 115 | 5% helix, 50% strand | — |
| C | Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera | protein | 361 | 20% helix, 41% strand | P03129, P16213, A0A678ZGP6 |
| E | Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera | protein | 368 | 19% helix, 41% strand | P03129, P16213, A0A678ZGP6 |
| G | Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera | protein | 366 | 20% helix, 41% strand | P03129, P16213, A0A678ZGP6 |
| I | Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera | protein | 358 | 20% helix, 41% strand | P03129, P16213, A0A678ZGP6 |
| K | Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera | protein | 376 | 20% helix, 40% strand | P03129, P16213, A0A678ZGP6 |
| M | Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera | protein | 372 | 19% helix, 41% strand | P03129, P16213, A0A678ZGP6 |
| O | Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera | protein | 361 | 20% helix, 41% strand | P03129, P16213, A0A678ZGP6 |
| Q | Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera | protein | 375 | 20% helix, 42% strand | P03129, P16213, A0A678ZGP6 |
| S | Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera | protein | 345 | 20% helix, 39% strand | P03129, P16213, A0A678ZGP6 |
| U | Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera | protein | 348 | 21% helix, 41% strand | P03129, P16213, A0A678ZGP6 |
| W | Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera | protein | 350 | 20% helix, 40% strand | P03129, P16213, A0A678ZGP6 |
| Y | Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera | protein | 376 | 20% helix, 42% strand | P03129, P16213, A0A678ZGP6 |
| a | Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera | protein | 357 | 20% helix, 39% strand | P03129, P16213, A0A678ZGP6 |
| c | Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera | protein | 352 | 20% helix, 40% strand | P03129, P16213, A0A678ZGP6 |
| e | Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera | protein | 354 | 20% helix, 41% strand | P03129, P16213, A0A678ZGP6 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.68 | 0.77 | 56 | empty |
| 2 | 576 | 0.68 | 0.78 | 62 | empty |
| 3 | 508 | 0.68 | 0.78 | 50 | empty |
| 4 | 589 | 0.68 | 0.77 | 56 | empty |
| 5 | 615 | 0.67 | 0.77 | 58 | empty |
Interfaces
52 interfaces between chains.
- c–d · 929 Ų buried · 18 hydrogen bonds · protein-protein
- M–N · 927 Ų buried · 20 hydrogen bonds · protein-protein
- I–J · 925 Ų buried · 15 hydrogen bonds · protein-protein
- O–P · 924 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 923 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 79 disulfide (disulfide).
Compared structures
- P16213 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P16213) · a predicted model of the same protein · chain S 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 7ST3 · PDBe 7ST3 · UniProt P03129 · UniProt P16213 · UniProt A0A678ZGP6
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