Research workbench
HLA-B*15:02 complexed with a synthetic peptide
Analyse HLA-B*15:02 complexed with a synthetic peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VB1
- Type
- protein
- Length
- 384 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Synthetic peptide…
- UniProt
- F4NBQ8, P61769
- Ligands
- NA
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 276 | 28% helix, 39% strand | F4NBQ8 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Synthetic peptide glu-leu-arg-ala-arg-glu-glu-ala-tyr | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 651 | 0.69 | 0.77 | 52 | EDO, GOL |
| 2 | 164 | 0.49 | 0.77 | 29 | EDO |
| 3 | 105 | 0.42 | 0.77 | 20 | empty |
| 4 | 76 | 0.39 | 0.78 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1278 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 942 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
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 F4NBQ8
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6VB1 · PDBe 6VB1 · UniProt F4NBQ8 · UniProt P61769
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