Research workbench
Crystal structure of HLA-B*2709 complexed with the vasoactive intestinal peptide type 1 receptor (vipr) peptide (residues 400-408)
Analyse Crystal structure of HLA-B*2709 complexed with the vasoactive intestinal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OF2
- Type
- protein
- Length
- 385 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human lymphocyte antigen HLA-B27; Beta-2-microglobulin; Vasoactive intestinal polypeptide…
- UniProt
- Q29846, P01884, P32241
- Ligands
- MN
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Human lymphocyte antigen HLA-B27 | protein | 276 | 25% helix, 39% strand | Q29846 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P01884 |
| C | Vasoactive intestinal polypeptide receptor | protein | 9 | 0% helix, 0% strand | P32241 |
Ligands and binding sites
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 | 615 | 0.68 | 0.77 | 54 | GOL |
| 2 | 103 | 0.46 | 0.79 | 21 | empty |
| 3 | 83 | 0.42 | 0.79 | 23 | empty |
| 4 | 80 | 0.39 | 0.77 | 16 | empty |
| 5 | 61 | 0.32 | 0.76 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1354 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1096 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1OF2 · Crystal structure of HLA-B*2709 complexed with the vasoactive intestinal peptide type 1… · the same entry in another collection · chain A against A, TM-score 1.00
- P32241 · AlphaFold monomer V2.0 prediction for vasoactive intestinal polypeptide receptor 1… · a predicted model of the same protein · chain C against A, TM-score 0.33
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 Q29846
- Every structure of UniProt P01884
- Every structure of UniProt P32241
- Elsewhere: RCSB PDB 1OF2 · PDBe 1OF2 · UniProt Q29846 · UniProt P01884 · UniProt P32241
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