Research workbench
Crystal Structure of HLA-B*57:01 with a modified HIV peptide RKV-Kyn
Analyse Crystal Structure of HLA-B*57:01 with a modified HIV peptide RKV-Kyn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BXP
- Type
- protein
- Length
- 380 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.45
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- HLA class I histocompatibility antigen, B-57 alpha chain; Beta-2-microglobulin; HIV…
- UniProt
- P18465, P61769
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · resolution 1.45 · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-57 alpha chain | protein | 275 | 27% helix, 39% strand | P18465 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | HIV peptide RKV-Kyn | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACT · Acetate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 603 | 0.68 | 0.77 | 51 | empty |
| 2 | 138 | 0.55 | 0.82 | 23 | empty |
| 3 | 96 | 0.42 | 0.78 | 23 | empty |
| 4 | 66 | 0.38 | 0.79 | 17 | empty |
| 5 | 72 | 0.36 | 0.77 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1375 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 860 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 6BXP · Crystal structure of HLA-B*57:01 with a modified HIV peptide rkv-kyn · 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 P18465
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6BXP · PDBe 6BXP · UniProt P18465 · UniProt P61769
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