MolNFT v1 · #38709 · protein
Crystal structure of HLA-B*3501 presenting the human cytochrome P450 derived peptide, kpivvlhgy
2H6P · HLA-B35: “Crystal structure of HLA-B*3501 presenting the human cytochrome P450 derived peptide, kpivvlhgy”. X-ray diffraction, 5 pockets (best druggability 0.68). MolNFT v1 #38709 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2H6P
- Type
- protein
- Length
- 384 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA-B35; Beta-2-microglobulin; 9 mer peptide from cytochrome P450
- UniProt
- O19626, P61769, P33260
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA-B35 | protein | 276 | 26% helix, 39% strand | O19626 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | 9 mer peptide from cytochrome P450 | protein | 9 | 0% helix, 0% strand | P33260 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.68 | 0.77 | 55 | empty |
| 2 | 128 | 0.44 | 0.77 | 24 | empty |
| 3 | 100 | 0.41 | 0.77 | 23 | empty |
| 4 | 82 | 0.41 | 0.79 | 16 | empty |
| 5 | 71 | 0.37 | 0.78 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1352 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 931 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2H6P · Crystal structure of HLA-B*3501 presenting the human cytochrome P450 derived 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
- P33260 · AlphaFold monomer V2.0 prediction for cytochrome P450 2C18 (P33260) · a predicted model of the same protein · chain C against A, TM-score 0.38
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 O19626
- Every structure of UniProt P61769
- Every structure of UniProt P33260
- Elsewhere: RCSB PDB 2H6P · PDBe 2H6P · UniProt O19626 · UniProt P61769 · UniProt P33260
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