Research workbench
Crystal structure of dual peptide from EBV in complex with HLA-A*11:01
Analyse Crystal structure of dual peptide from EBV in complex with HLA-A*11:01 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GRG
- Type
- protein
- Length
- 383 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-11 alpha chain; Beta-2-microglobulin; Epstein…
- UniProt
- P13746, P61769
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-11 alpha chain | protein | 274 | 27% helix, 39% strand | P13746 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Epstein barr virus, latent membrane protein 2 epitope | protein | 6 | 0% helix, 0% strand | — |
| D | Epstein barr virus, latent membrane protein 2 epitope | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · 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 | 576 | 0.67 | 0.77 | 51 | GOL |
| 2 | 193 | 0.52 | 0.78 | 31 | GOL |
| 3 | 50 | 0.34 | 0.79 | 15 | empty |
| 4 | 53 | 0.28 | 0.75 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1416 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 458 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 392 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 47 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5GRG · Crystal structure of dual peptide from EBV in complex with HLA-A*11:01 · the same entry in another collection · chain A against A, TM-score 1.00
- 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 P13746
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 5GRG · PDBe 5GRG · UniProt P13746 · UniProt P61769
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