MolNFT v1 · #173016 · protein
Structure of B*27:09/PHOTORL9
7ALO · Lymphocyte antigen HLA-B27: “Structure of B*27:09/PHOTORL9”. X-ray diffraction, 1 ligand (PRQ), 12 pockets (best druggability 0.75). MolNFT v1 #173016 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7ALO
- Type
- protein
- Length
- 766 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lymphocyte antigen HLA-B27; Beta-2-microglobulin; Vasoactive intestinal polypeptide…
- UniProt
- A0A2R7Z5J3, P61769, P32241
- Ligands
- PRQ
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Lymphocyte antigen HLA-B27 | protein | 276 | 27% helix, 41% strand | A0A2R7Z5J3 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C, F | Vasoactive intestinal polypeptide receptor 1 | protein | 8 | 0% helix, 0% strand | P32241 |
Ligands and binding sites
- PRQ · (3S)-3-amino-3-(2-nitrophenyl)propanoic acid · ligand · 2 copies · chains A, C, D, F
- GOL · Glycerol · additive · 12 copies · chains A, B, D, E
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B, E, D
- 1PE · Pentaethylene glycol · additive · chains A, B
- PGE · Triethylene glycol · additive · chains B
- PEG · Di(hydroxyethyl)ether · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 582 | 0.75 | 0.82 | 58 | empty |
| 2 | 540 | 0.72 | 0.81 | 57 | TRS, GOL |
| 3 | 504 | 0.72 | 0.81 | 49 | GOL |
| 4 | 492 | 0.72 | 0.81 | 48 | GOL |
| 5 | 158 | 0.63 | 0.85 | 27 | PRQ |
Interfaces
7 interfaces between chains.
- D–E · 1318 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1304 Ų buried · 25 hydrogen bonds · protein-protein
- D–F · 988 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 949 Ų buried · 22 hydrogen bonds · protein-protein
- B–E · 424 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 covalent (disulfide, covalent ligand).
Compared structures
- 7ALO · Structure of B*27:09/photoRL9 · the same entry in another collection · chain C against C, 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 0.36
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 A0A2R7Z5J3
- Every structure of UniProt P61769
- Every structure of UniProt P32241
- Elsewhere: RCSB PDB 7ALO · PDBe 7ALO · UniProt A0A2R7Z5J3 · UniProt P61769 · UniProt P32241
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