MolNFT v2 · #225446 · protein
Fab M2-7 complexed with SARS-Cov2 RBD and human ACE2
8XXW · Processed angiotensin-converting enzyme 2: “Fab M2-7 complexed with SARS-Cov2 RBD and human ACE2”. Electron microscopy at 3.03, 2 ligands (NAG, ZN), 10 pockets (best druggability 0.71). MolNFT v2 #225446 on GenesisL1: 3D structure…
- PDB
- 8XXW
- Type
- protein
- Length
- 950 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.03
- Source
- Homo sapiens; Mus musculus; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Processed angiotensin-converting enzyme 2; Spike protein S1; M2-7-Heavy chain; M2-7-Light…
- UniProt
- Q9BYF1, P0DTC2
- Ligands
- NAG, ZN
- Pockets
- 10 · best druggability 0.71
Structure
electron microscopy · resolution 3.03 · 4 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Processed angiotensin-converting enzyme 2 | protein | 561 | 64% helix, 3% strand | Q9BYF1 |
| E | Spike protein S1 | protein | 162 | 15% helix, 28% strand | P0DTC2 |
| H | M2-7-Heavy chain | protein | 120 | 10% helix, 49% strand | — |
| L | M2-7-Light chain | protein | 107 | 3% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, E
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 604 | 0.71 | 0.79 | 65 | empty |
| 2 | 546 | 0.70 | 0.79 | 55 | ZN |
| 3 | 430 | 0.63 | 0.77 | 48 | empty |
| 4 | 210 | 0.59 | 0.81 | 30 | empty |
| 5 | 214 | 0.55 | 0.78 | 28 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1004 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 863 Ų buried · 11 hydrogen bonds · protein-protein
- E–H · 618 Ų buried · 6 hydrogen bonds · protein-protein
- E–L · 187 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.99
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.99
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.98
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.98
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.98
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · 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 A 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 Q9BYF1
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 8XXW · PDBe 8XXW · UniProt Q9BYF1 · UniProt P0DTC2
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