MolNFT v1 · #176170 · protein
Cryo-EM structure of human ACE2 and GX/P2V/2017 rbd
7DDP · Angiotensin-converting enzyme 2: “Cryo-EM structure of human ACE2 and GX/P2V/2017 rbd”. Electron microscopy, 2 ligands (NAG, ZN), 7 pockets (best druggability 0.70). MolNFT v1 #176170 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7DDP
- Type
- protein
- Length
- 791 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Angiotensin-converting enzyme 2; Spike protein S1
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- Q9BYF1, A0A6G6A1M4
- Ligands
- NAG, ZN
- Pockets
- 7 · best druggability 0.70
Structure
electron microscopy · 2 distinct chains · 49% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 597 | 61% helix, 3% strand | Q9BYF1 |
| C | Spike protein S1 | protein | 194 | 12% helix, 27% strand | A0A6G6A1M4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, C
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 524 | 0.70 | 0.80 | 69 | empty |
| 2 | 305 | 0.64 | 0.81 | 32 | empty |
| 3 | 292 | 0.56 | 0.76 | 38 | empty |
| 4 | 71 | 0.39 | 0.78 | 16 | empty |
| 5 | 76 | 0.38 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–C · 925 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 7DDP · Cryo-EM structure of human ACE2 and GX/P2V/2017 RBD · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.99
- 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 0.99
- 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
- 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
- 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 0.99
- 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 0.99
- 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 0.97
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 A0A6G6A1M4
- Elsewhere: RCSB PDB 7DDP · PDBe 7DDP · UniProt Q9BYF1 · UniProt A0A6G6A1M4
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