MolNFT v1 · #146652 · protein
Structure of nanobody-stabilized angiotensin II type 1 receptor bound to S1I8
6DO1 · Type-1 angiotensin II RECEPTOR,SOLUBLE cytochrome B562 bril…: “Structure of nanobody-stabilized angiotensin II type 1 receptor bound to S1I8”. X-ray diffraction, 2 ligands (NAG, CL), 18 pockets (best druggability 0.67). MolNFT v1…
- PDB
- 6DO1
- Type
- protein
- Length
- 1,008 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type-1 angiotensin II RECEPTOR,SOLUBLE cytochrome B562 bril fusion protein; Nanobody…
- UniProt
- P30556, P0ABE7
- Ligands
- NAG, CL
- Pockets
- 18 · best druggability 0.67
Structure
x-ray diffraction · 6 distinct chains · 35% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Type-1 angiotensin II RECEPTOR,SOLUBLE cytochrome B562 bril fusion protein | protein | 304 | 76% helix, 5% strand | P30556, P0ABE7 |
| C | Nanobody NB.AT110I1 | protein | 125 | 5% helix, 54% strand | — |
| D | Nanobody NB.AT110I1 | protein | 126 | 5% helix, 54% strand | — |
| E | Nanobody NB.AT110I1 | protein | 58 | 0% helix, 38% strand | — |
| F | Nanobody NB.AT110I1 | protein | 75 | 4% helix, 45% strand | — |
| G, H | Angiotensin-like peptide S1I8 | protein | 8 | 0% helix, 38% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, C, B, D
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.67 | 0.93 | 25 | empty |
| 2 | 359 | 0.62 | 0.78 | 36 | empty |
| 3 | 172 | 0.58 | 0.82 | 27 | empty |
| 4 | 407 | 0.57 | 0.74 | 52 | empty |
| 5 | 282 | 0.52 | 0.75 | 35 | empty |
Interfaces
10 interfaces between chains.
- B–D · 1213 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1178 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 915 Ų buried · 15 hydrogen bonds · protein-protein
- B–G · 901 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 563 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan, 2 modified (disulfide, N-glycosylation, methylation).
Compared structures
- 6DO1 · Structure of nanobody-stabilized angiotensin II type 1 receptor bound to S1I8 · the same entry in another collection · chain H against H, TM-score 1.00
- P30556 · AlphaFold monomer V2.0 prediction for type-1 angiotensin II receptor (P30556) · a predicted model of the same protein · chain B against A, TM-score 0.90
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain B against A, TM-score 0.27
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 P30556
- Every structure of UniProt P0ABE7
- Elsewhere: RCSB PDB 6DO1 · PDBe 6DO1 · UniProt P30556 · UniProt P0ABE7
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