MolNFT v1 · #12724 · protein
The human non-classical major histocompatibility complex molecule HLA- E
1KPR · HLA class I histocompatibility antigen, alpha chain: “The human non-classical major histocompatibility complex molecule HLA- E”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.66). MolNFT v1 #12724 on GenesisL1…
- PDB
- 1KPR
- Type
- protein
- Length
- 766 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, alpha chain; Beta-2-microglobulin; Peptide…
- UniProt
- P13747, P61769
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | HLA class I histocompatibility antigen, alpha chain | protein | 274 | 26% helix, 40% 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
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 639 | 0.66 | 0.76 | 59 | empty |
| 2 | 526 | 0.66 | 0.77 | 47 | empty |
| 3 | 126 | 0.59 | 0.85 | 30 | empty |
| 4 | 93 | 0.54 | 0.84 | 25 | empty |
| 5 | 130 | 0.46 | 0.78 | 20 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1397 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1362 Ų buried · 27 hydrogen bonds · protein-protein
- A–P · 902 Ų buried · 12 hydrogen bonds · protein-protein
- C–Q · 896 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 697 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1KPR · 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 B 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 0.96
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 1KPR · PDBe 1KPR · UniProt P13747 · UniProt P61769
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