Research workbench
Crystal structure of HLA-B*2709 complexed with the latent membrane protein 2 peptide (LMP2) of epstein-barr virus
Analyse Crystal structure of HLA-B*2709 complexed with the latent membrane protein 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UXW
- 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-27 alpha chain; Beta-2-microglobulin; Gene…
- UniProt
- P03989, P01884, P13285
- 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-27 alpha chain | protein | 276 | 28% helix, 40% strand | P03989 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P01884 |
| C | Gene terminal protein (membrane protein lmp-2A/LMP-2B) | protein | 9 | 0% helix, 0% strand | P13285 |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains A, B, C
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 | 64 | 0.70 | 0.97 | 16 | GOL |
| 2 | 638 | 0.69 | 0.77 | 63 | GOL |
| 3 | 112 | 0.48 | 0.80 | 21 | empty |
| 4 | 82 | 0.38 | 0.77 | 16 | empty |
| 5 | 61 | 0.28 | 0.73 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1342 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1078 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1UXW · Crystal structure of HLA-B*2709 complexed with the latent membrane protein 2 peptide… · the same entry in another collection · chain A against A, TM-score 1.00
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 P03989
- Every structure of UniProt P01884
- Every structure of UniProt P13285
- Elsewhere: RCSB PDB 1UXW · PDBe 1UXW · UniProt P03989 · UniProt P01884 · UniProt P13285
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