MolNFT v1 · #121965 · protein
Crystal structure of HLA-B*27:05 complexed with the self-peptide pvipr and nickel
5IB4 · HLA class I histocompatibility antigen, B-27 alpha chain: “Crystal structure of HLA-B*27:05 complexed with the self-peptide pvipr and nickel”. X-ray diffraction, 1 ligand (NI), 5 pockets (best druggability 0.67). MolNFT v1 #121965…
- PDB
- 5IB4
- 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…
- UniProt
- P03989, P61769, P32241
- Ligands
- NI
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-27 alpha chain | protein | 276 | 27% helix, 39% strand | P03989 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Vasoactive intestinal polypeptide receptor 1 | protein | 9 | 0% helix, 0% strand | P32241 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains A, C
- GOL · Glycerol · additive · 2 copies · 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 | 596 | 0.67 | 0.77 | 56 | GOL |
| 2 | 102 | 0.46 | 0.80 | 19 | empty |
| 3 | 60 | 0.41 | 0.81 | 17 | empty |
| 4 | 67 | 0.33 | 0.76 | 15 | empty |
| 5 | 50 | 0.29 | 0.76 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1354 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1108 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5IB4 · Crystal structure of HLA-B*27:05 complexed with the self-peptide pVIPR and Nickel · 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 0.99
- 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 5IB4 · PDBe 5IB4 · UniProt P03989 · UniProt P61769 · UniProt P32241
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.