Research workbench
Crystal structure of peptide VSFIEFVGW in complex with HLA-B5801
Analyse Crystal structure of peptide VSFIEFVGW 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
- 7X00
- Type
- protein
- Length
- 385 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.45
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Val-ser-phe-ile-glu-phe-val-gly-TRP
- UniProt
- F4NC28, P61769
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · resolution 1.45 · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 277 | 28% helix, 39% strand | F4NC28 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Val-ser-phe-ile-glu-phe-val-gly-TRP | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.69 | 0.77 | 59 | GOL |
| 2 | 208 | 0.52 | 0.77 | 36 | empty |
| 3 | 102 | 0.43 | 0.78 | 23 | empty |
| 4 | 77 | 0.37 | 0.77 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1332 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 864 Ų buried · 13 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 0.99
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 7X00 · PDBe 7X00 · UniProt F4NC28 · UniProt P61769
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