Research workbench
ACE2 -targeting monoclonal antibody as potent and broad-spectrum coronavirus blocker
Analyse ACE2 -targeting monoclonal antibody as potent and broad-spectrum coronavirus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V61
- Type
- protein
- Length
- 3,586 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium-dependent neutral amino acid transporter B(0)AT1; Angiotensin-converting enzyme 2…
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- Q695T7, Q9BYF1
- Ligands
- NAG, ZN
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 4 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Sodium-dependent neutral amino acid transporter B(0)AT1 | protein | 605 | 62% helix, 0% strand | Q695T7 |
| B, D | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 751 | 54% helix, 6% strand | Q9BYF1 |
| H, I | 3E8 | protein | 223 | 4% helix, 46% strand | — |
| K, M | 3E8 | protein | 214 | 5% helix, 38% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 38 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.77 | 0.79 | 78 | empty |
| 2 | 1012 | 0.76 | 0.78 | 70 | empty |
| 3 | 836 | 0.69 | 0.76 | 70 | ZN |
| 4 | 59 | 0.68 | 0.95 | 22 | empty |
| 5 | 402 | 0.67 | 0.80 | 51 | empty |
Interfaces
9 interfaces between chains.
- H–K · 2020 Ų buried · 15 hydrogen bonds · protein-protein
- I–M · 2008 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1354 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1341 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1335 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 glycan, 18 disulfide (N-glycosylation, disulfide).
Compared structures
- 7V61 · ACE2 -Targeting Monoclonal Antibody as Potent and Broad-Spectrum Coronavirus Blocker · the same entry in another collection · chain A against A, TM-score 1.00
- Q695T7 · AlphaFold monomer V2.0 prediction for sodium-dependent neutral amino acid transporter… · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain D against A, TM-score 0.95
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain B against A, TM-score 0.79
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 Q695T7
- Every structure of UniProt Q9BYF1
- Elsewhere: RCSB PDB 7V61 · PDBe 7V61 · UniProt Q695T7 · UniProt Q9BYF1
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