Research workbench
The human non-classical major histocompatibility complex molecule HLA-E
Analyse The human non-classical major histocompatibility complex molecule HLA-E in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MHE
- Type
- protein
- Length
- 764 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen HLA-E; Beta-2-microglobulin; Peptide (vmaprtvll)
- UniProt
- P13747, P61769
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | HLA class I histocompatibility antigen HLA-E | protein | 273 | 26% helix, 38% strand | P13747 |
| B, D | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| P, Q | Peptide (vmaprtvll) | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.69 | 0.77 | 60 | empty |
| 2 | 679 | 0.68 | 0.76 | 60 | empty |
| 3 | 143 | 0.63 | 0.86 | 27 | empty |
| 4 | 113 | 0.59 | 0.86 | 27 | empty |
| 5 | 145 | 0.48 | 0.78 | 20 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1420 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1391 Ų buried · 22 hydrogen bonds · protein-protein
- A–P · 905 Ų buried · 13 hydrogen bonds · protein-protein
- C–Q · 886 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 662 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1MHE · The human non-classical major histocompatibility complex molecule HLA-E · the same entry in another collection · chain Q against Q, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain D against A, TM-score 0.99
- P13747 · AlphaFold monomer V2.0 prediction for HLA class I histocompatibility antigen, alpha chain… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P13747
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 1MHE · PDBe 1MHE · UniProt P13747 · UniProt P61769
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