Research workbench
Crystal Structure of HLA B*3508 in complex with a HCMV 12-mer peptide from the pp65 protein
Analyse Crystal Structure of HLA B*3508 in complex with a HCMV 12-mer peptide from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BW9
- Type
- protein
- Length
- 388 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.75
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- HLA class I histocompatibility antigen, B-35 alpha chain; Beta-2-microglobulin; CPS…
- UniProt
- P30685, P61769, P06725
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · resolution 1.75 · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-35 alpha chain | protein | 276 | 26% helix, 40% strand | P30685 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | CPS peptide from 65 kDa lower matrix phosphoprotein | protein | 12 | 33% helix, 0% strand | P06725 |
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 | 600 | 0.69 | 0.78 | 49 | empty |
| 2 | 196 | 0.53 | 0.78 | 37 | empty |
| 3 | 114 | 0.42 | 0.77 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1373 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 957 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3BW9 · Crystal structure of HLA B*3508 in complex with a hcmv 12-mer peptide from the PP65… · 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 0.98
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 P30685
- Every structure of UniProt P61769
- Every structure of UniProt P06725
- Elsewhere: RCSB PDB 3BW9 · PDBe 3BW9 · UniProt P30685 · UniProt P61769 · UniProt P06725
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