Research workbench
Crystal structure of HLA-B*27:09 complexed with the self-peptide pvipr and copper
Analyse Crystal structure of HLA-B*27:09 complexed with the self-peptide pvipr and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IB5
- Type
- protein
- Length
- 770 residues
- Chains
- 6
- 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…
- UniProt
- P03989, P61769, P32241
- Ligands
- CU, CL
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen, B-27 alpha chain | protein | 276 | 26% helix, 39% strand | P03989 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | Vasoactive intestinal polypeptide receptor 1 | protein | 9 | 0% helix, 0% strand | P32241 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 6 copies · chains A, E, C, D, F
- CL · Chloride ion · ion · chains D, F
- GOL · Glycerol · additive · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.69 | 0.75 | 77 | empty |
| 2 | 542 | 0.68 | 0.78 | 47 | GOL |
| 3 | 625 | 0.68 | 0.77 | 56 | empty |
| 4 | 144 | 0.49 | 0.78 | 21 | empty |
| 5 | 121 | 0.47 | 0.79 | 18 | empty |
Interfaces
7 interfaces between chains.
- D–E · 1429 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1402 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1118 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 1113 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 325 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5IB5 · Crystal structure of HLA-B*27:09 complexed with the self-peptide pVIPR and Copper · the same entry in another collection · chain F against F, 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
- 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 0.32
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
- Every structure of UniProt P32241
- Elsewhere: RCSB PDB 5IB5 · PDBe 5IB5 · UniProt P03989 · UniProt P61769 · UniProt P32241
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