MolNFT v1 · #122078 · protein
Structure of HLA-B*40:02 in complex with the endogenous peptide refskepel
5IEK · HLA class I histocompatibility antigen, B-40 alpha chain: “Structure of HLA-B*40:02 in complex with the endogenous peptide refskepel”. X-ray diffraction, 3 pockets (best druggability 0.69). MolNFT v1 #122078 on GenesisL1: 3D…
- PDB
- 5IEK
- Type
- protein
- Length
- 385 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-40 alpha chain; Beta-2-microglobulin…
- UniProt
- Q04826, P61769
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-40 alpha chain | protein | 276 | 27% helix, 39% strand | Q04826 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Arg-glu-phe-ser-lys-glu-pro-glu-leu | protein | 9 | 0% helix, 0% strand | — |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.69 | 0.77 | 55 | empty |
| 2 | 219 | 0.56 | 0.79 | 41 | empty |
| 3 | 93 | 0.44 | 0.79 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1319 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 965 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5IEK · Structure of HLA-B*40:02 in complex with the endogenous peptide REFSKEPEL · 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 0.99
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 Q04826
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 5IEK · PDBe 5IEK · UniProt Q04826 · UniProt P61769
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