Research workbench
Crystal structure of HLA B*3508LPEP-P5ALA , peptide mutant P5-ala
Analyse Crystal structure of HLA B*3508LPEP-P5ALA , peptide mutant P5-ala in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VFS
- Type
- protein
- Length
- 388 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Lpep peptide from EBV, P5A, lpepapqgqltay
- UniProt
- C5MK56, P61769
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 276 | 26% helix, 39% strand | C5MK56 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Lpep peptide from EBV, P5A, lpepapqgqltay | protein | 13 | 0% helix, 0% strand | — |
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 | 636 | 0.69 | 0.78 | 54 | empty |
| 2 | 65 | 0.59 | 0.90 | 20 | empty |
| 3 | 84 | 0.42 | 0.79 | 23 | empty |
| 4 | 95 | 0.38 | 0.76 | 23 | empty |
| 5 | 78 | 0.37 | 0.77 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1376 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 956 Ų buried · 18 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 C5MK56
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 3VFS · PDBe 3VFS · UniProt C5MK56 · UniProt P61769
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