MolNFT v1 · #27689 · protein
Crystal structures of HLA-B*1501 in complex with peptides from human UBCH6 and epstein-barr virus ebna-3
1XR9 · HLA class I histocompatibility antigen, B-15 alpha chain: “Crystal structures of HLA-B*1501 in complex with peptides from human UBCH6 and epstein-barr virus ebna-3”. X-ray diffraction, 2 ligands (URE, SO4), 5 pockets (best…
- PDB
- 1XR9
- Type
- protein
- Length
- 384 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-15 alpha chain; Beta-2-microglobulin…
- EC
- 6.3.2.19
- UniProt
- P30464, P61769, P51965
- Ligands
- URE, SO4
- Pockets
- 5 · best druggability 0.70
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-15 alpha chain | protein | 276 | 27% helix, 39% strand | P30464 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Ubiquitin-conjugating enzyme E2 E1 (EC 6.3.2.19) | protein | 9 | 0% helix, 0% strand | P51965 |
Ligands and binding sites
- URE · Urea · ligand · chains A, B
- SO4 · Sulfate ion · ion · 2 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
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 631 | 0.70 | 0.78 | 55 | GOL, SO4 |
| 2 | 162 | 0.47 | 0.77 | 28 | empty |
| 3 | 107 | 0.44 | 0.78 | 24 | URE |
| 4 | 71 | 0.40 | 0.79 | 16 | empty |
| 5 | 59 | 0.32 | 0.76 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1341 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 875 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1XR9 · Crystal Structures of HLA-B*1501 in Complex with Peptides from Human UbcH6 and… · 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
- P51965 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 E1 (P51965) · a predicted model of the same protein · chain C against A, TM-score 0.36
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 P30464
- Every structure of UniProt P61769
- Every structure of UniProt P51965
- Elsewhere: RCSB PDB 1XR9 · PDBe 1XR9 · UniProt P30464 · UniProt P61769 · UniProt P51965
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