Research workbench
Crystal structure of HLA-B7 with the hcmv PP65 peptide rpherngftvl
Analyse Crystal structure of HLA-B7 with the hcmv PP65 peptide rpherngftvl in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VCL
- 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-7 alpha chain; Beta-2-microglobulin; Peptide…
- UniProt
- P01889, P61769, F5HB26
- Ligands
- NI
- Pockets
- 3 · best druggability 0.67
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-7 alpha chain | protein | 275 | 28% helix, 40% strand | P01889 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Peptide from tegument protein PP65 | protein | 11 | 0% helix, 0% strand | F5HB26 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
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 | 412 | 0.67 | 0.80 | 45 | GOL |
| 2 | 162 | 0.49 | 0.77 | 26 | empty |
| 3 | 73 | 0.39 | 0.78 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1328 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 965 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3VCL · Crystal Structure of HLA-B7 with the HCMV pp65 peptide RPHERNGFTVL · 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
- P01889 · AlphaFold monomer V2.0 prediction for HLA class I histocompatibility antigen, B alpha… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P01889
- Every structure of UniProt P61769
- Every structure of UniProt F5HB26
- Elsewhere: RCSB PDB 3VCL · PDBe 3VCL · UniProt P01889 · UniProt P61769 · UniProt F5HB26
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