MolNFT v1 · #154959 · protein
Crystal structure of the human adiponectin receptor 1 D208A mutant
6KRZ · Adiponectin receptor protein 1: “Crystal structure of the human adiponectin receptor 1 D208A mutant”. X-ray diffraction, 4 ligands (OLA, OLB, ZN), 15 pockets (best druggability 0.87). MolNFT v1 #154959 on GenesisL1: 3D structure…
- PDB
- 6KRZ
- Type
- protein
- Length
- 1,526 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adiponectin receptor protein 1; The heavy chain variable domain (antibody); The light…
- UniProt
- Q96A54
- Ligands
- OLA, OLB, ZN, PO4
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adiponectin receptor protein 1 | protein | 284 | 72% helix, 1% strand | Q96A54 |
| B, C | Adiponectin receptor protein 1 | protein | 282 | 75% helix, 1% strand | Q96A54 |
| D, F, H | The heavy chain variable domain (antibody) | protein | 119 | 8% helix, 48% strand | — |
| E, G, I | The light chain variable domain (antibody) | protein | 107 | 0% helix, 50% strand | — |
Ligands and binding sites
- OLA · Oleic acid · ligand · 2 copies · chains A
- OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · 2 copies · chains C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, E, B, G, C, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 493 | 0.87 | 0.94 | 73 | OLA |
| 2 | 543 | 0.82 | 0.88 | 69 | ZN |
| 3 | 862 | 0.76 | 0.79 | 68 | ZN, OLB |
| 4 | 761 | 0.70 | 0.77 | 76 | empty |
| 5 | 69 | 0.69 | 0.95 | 17 | empty |
Interfaces
15 interfaces between chains.
- H–I · 795 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 784 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 773 Ų buried · 5 hydrogen bonds · protein-protein
- C–I · 533 Ų buried · 8 hydrogen bonds · protein-protein
- B–G · 522 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6KRZ · Crystal structure of the human adiponectin receptor 1 D208A mutant · the same entry in another collection · chain I against I, TM-score 1.00
- Q96A54 · AlphaFold monomer V2.0 prediction for adiponectin receptor protein 1 (Q96A54) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q96A54
- Elsewhere: RCSB PDB 6KRZ · PDBe 6KRZ · UniProt Q96A54
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.