Research workbench
Structure of apelin receptor in complex with agonist peptide
Analyse Structure of apelin receptor in complex with agonist peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VBL
- Type
- protein
- Length
- 370 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agonist peptide; Apelin RECEPTOR,RUBREDOXIN,APELIN receptor chimera
- UniProt
- P35414, P00268
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 64% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Agonist peptide | protein | 17 | 0% helix, 6% strand | — |
| B | Apelin RECEPTOR,RUBREDOXIN,APELIN receptor chimera | protein | 353 | 67% helix, 5% strand | P35414, P00268 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains B
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.73 | 0.93 | 37 | OLC |
| 2 | 187 | 0.52 | 0.78 | 24 | empty |
| 3 | 97 | 0.47 | 0.80 | 16 | empty |
| 4 | 57 | 0.47 | 0.84 | 14 | empty |
| 5 | 101 | 0.40 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1206 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified, 2 disulfide, 1 isopeptide (nonstandard, disulfide, isopeptide).
Compared structures
- 5VBL · Structure of apelin receptor in complex with agonist peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P35414 · AlphaFold monomer V2.0 prediction for apelin receptor (P35414) · a predicted model of the same protein · chain B against A, TM-score 0.85
- P00268 · AlphaFold monomer V2.0 prediction for rubredoxin (P00268) · a predicted model of the same protein · chain B against A, TM-score 0.15
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 P35414
- Every structure of UniProt P00268
- Elsewhere: RCSB PDB 5VBL · PDBe 5VBL · UniProt P35414 · UniProt P00268
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