Research workbench
Crystal structure of HLA-B*2709 complexed with a variant of the latent membrane protein 2 peptide (LMP2(L)) of epstein-barr virus
Analyse Crystal structure of HLA-B*2709 complexed with a variant of the latent membrane… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D18
- 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; Latent…
- UniProt
- P03989, P61769
- Pockets
- 6 · 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, 39% strand | P03989 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Latent membrane protein 2 | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, C, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.70 | 0.95 | 21 | GOL |
| 2 | 696 | 0.69 | 0.77 | 59 | TRS, MES |
| 3 | 143 | 0.49 | 0.79 | 20 | empty |
| 4 | 84 | 0.43 | 0.79 | 23 | GOL |
| 5 | 73 | 0.37 | 0.77 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1370 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1039 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3D18 · Crystal structure of HLA-B*2709 complexed with a variant of the latent membrane protein 2… · 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
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 P61769
- Elsewhere: RCSB PDB 3D18 · PDBe 3D18 · UniProt P03989 · UniProt P61769
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