MolNFT v1 · #160130 · protein
Crystal structure of HLA-A*68:01 in complex with NP145-156, a 12 mer influenza peptide
6PBH · HLA class I histocompatibility antigen, a-68 alpha chain: “Crystal structure of HLA-A*68:01 in complex with NP145-156, a 12 mer influenza peptide”. X-ray diffraction, 3 ligands (MG, SO4, IOD), 3 pockets (best druggability 0.67).…
- PDB
- 6PBH
- Type
- protein
- Length
- 378 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-68 alpha chain; Beta-2-microglobulin; Influenza…
- UniProt
- P01891, P61769
- Ligands
- MG, SO4, IOD
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-68 alpha chain | protein | 274 | 27% helix, 41% strand | P01891 |
| B | Beta-2-microglobulin | protein | 97 | 0% helix, 48% strand | P61769 |
| C | Influenza a NP145-156 peptide | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- IOD · Iodide ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 601 | 0.67 | 0.77 | 60 | SO4 |
| 2 | 107 | 0.40 | 0.76 | 18 | empty |
| 3 | 56 | 0.34 | 0.78 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1230 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 775 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6PBH · Crystal Structure of HLA-A*68:01 in complex with NP145-156, a 12 mer influenza 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 P01891
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6PBH · PDBe 6PBH · UniProt P01891 · UniProt P61769
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