Research workbench
Crystal structure of peptide KAGQVVTIW in complex with HLA-B5801
Analyse Crystal structure of peptide KAGQVVTIW in complex with HLA-B5801 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WZZ
- Type
- protein
- Length
- 385 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.305
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Lys-ala-gly-gln-val-val-thr-ile-TRP
- UniProt
- F4NC28, P61769
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · resolution 1.305 · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 277 | 27% helix, 40% strand | F4NC28 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Lys-ala-gly-gln-val-val-thr-ile-TRP | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, C, B
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 | 666 | 0.68 | 0.77 | 61 | GOL |
| 2 | 169 | 0.48 | 0.77 | 29 | empty |
| 3 | 77 | 0.44 | 0.81 | 18 | empty |
| 4 | 72 | 0.36 | 0.77 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1348 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 847 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B 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 F4NC28
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 7WZZ · PDBe 7WZZ · UniProt F4NC28 · UniProt P61769
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