MolNFT v1 · #154829 · protein
Apelin receptor in complex with single domain antibody
6KNM · Apelin RECEPTOR,RUBREDOXIN,APELIN receptor: “Apelin receptor in complex with single domain antibody”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.74). MolNFT v1 #154829 on GenesisL1: 3D structure, binding sites…
- PDB
- 6KNM
- Type
- protein
- Length
- 480 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apelin RECEPTOR,RUBREDOXIN,APELIN receptor; Single domain antibody JN241
- UniProt
- P35414, P00268
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Apelin RECEPTOR,RUBREDOXIN,APELIN receptor | protein | 351 | 64% helix, 6% strand | P35414, P00268 |
| A | Single domain antibody JN241 | protein | 129 | 2% helix, 43% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.74 | 0.89 | 38 | empty |
| 2 | 75 | 0.67 | 0.93 | 26 | empty |
| 3 | 148 | 0.41 | 0.74 | 24 | empty |
| 4 | 89 | 0.36 | 0.75 | 19 | empty |
| 5 | 58 | 0.35 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- B–A · 1709 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6KNM · Apelin receptor in complex with single domain antibody · the same entry in another collection · chain B against B, 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 0.83
- 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 6KNM · PDBe 6KNM · UniProt P35414 · UniProt P00268
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