Research workbench
Nonstandard peptide binding of HLA-B*5101 complexed with HIV immunodominant epitope KM1(LPPVVAKEI)
Analyse Nonstandard peptide binding of HLA-B*5101 complexed with HIV immunodominant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1E27
- Type
- protein
- Length
- 384 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen heavy chain; Beta-2 microglobulin light chain…
- UniProt
- P18464, P01884, P24740
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen heavy chain | protein | 276 | 28% helix, 39% strand | P18464 |
| B | Beta-2 microglobulin light chain | protein | 99 | 0% helix, 49% strand | P01884 |
| C | HIV-1 peptide (lppvvakei) | protein | 9 | 0% helix, 0% strand | P24740 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 597 | 0.68 | 0.78 | 53 | empty |
| 2 | 88 | 0.50 | 0.82 | 20 | empty |
| 3 | 181 | 0.49 | 0.77 | 31 | empty |
| 4 | 73 | 0.43 | 0.81 | 23 | empty |
| 5 | 75 | 0.36 | 0.76 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1276 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 853 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1E27 · Nonstandard peptide binding of HLA-B*5101 complexed with HIV immunodominant epitope… · the same entry in another collection · chain A against A, TM-score 1.00
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 P18464
- Every structure of UniProt P01884
- Every structure of UniProt P24740
- Elsewhere: RCSB PDB 1E27 · PDBe 1E27 · UniProt P18464 · UniProt P01884 · UniProt P24740
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