MolNFT v1 · #122075 · protein
Structure of HLA-B*40:02 in complex with the phosphorylated endogenous peptide REF(P)SKEPEL
5IEH · HLA class I histocompatibility antigen, B-40 alpha chain: “Structure of HLA-B*40:02 in complex with the phosphorylated endogenous peptide REF(P)SKEPEL”. X-ray diffraction, 4 pockets (best druggability 0.68). MolNFT v1 #122075 on…
- PDB
- 5IEH
- Type
- protein
- Length
- 383 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; Inner…
- UniProt
- Q04826, P61769, E9PM67
- Pockets
- 4 · 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, B-40 alpha chain | protein | 276 | 28% helix, 39% strand | Q04826 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P61769 |
| C | Inner centromere protein | protein | 9 | 0% helix, 0% strand | E9PM67 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 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 | 626 | 0.68 | 0.77 | 55 | empty |
| 2 | 135 | 0.50 | 0.80 | 28 | empty |
| 3 | 85 | 0.41 | 0.79 | 24 | EDO |
| 4 | 58 | 0.28 | 0.74 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1277 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 946 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 modified (disulfide, phosphorylation).
Compared structures
- 5IEH · Structure of HLA-B*40:02 in complex with the phosphorylated endogenous peptide… · 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
- Every structure of UniProt E9PM67
- Elsewhere: RCSB PDB 5IEH · PDBe 5IEH · UniProt Q04826 · UniProt P61769 · UniProt E9PM67
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