MolNFT v1 · #186794 · protein
Crystal structure of affinity-enhancing and catalytically inactive ACE2 in complex with SARS-cov-2 rbd
7RPV · Processed angiotensin-converting enzyme 2: “Crystal structure of affinity-enhancing and catalytically inactive ACE2 in complex with SARS-cov-2 rbd”. X-ray diffraction, 2 ligands (NAG, ZN), 20 pockets (best druggability 0.83). MolNFT…
- PDB
- 7RPV
- Type
- protein
- Length
- 3,125 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Processed angiotensin-converting enzyme 2; Spike protein S1
- UniProt
- Q9BYF1, P0DTC2
- Ligands
- NAG, ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Processed angiotensin-converting enzyme 2 | protein | 597 | 60% helix, 4% strand | Q9BYF1 |
| E | Spike protein S1 | protein | 187 | 17% helix, 26% strand | P0DTC2 |
| F | Spike protein S1 | protein | 184 | 20% helix, 23% strand | P0DTC2 |
| C | Processed angiotensin-converting enzyme 2 | protein | 595 | 63% helix, 4% strand | Q9BYF1 |
| G | Spike protein S1 | protein | 184 | 11% helix, 23% strand | P0DTC2 |
| D | Processed angiotensin-converting enzyme 2 | protein | 596 | 62% helix, 5% strand | Q9BYF1 |
| H | Spike protein S1 | protein | 185 | 13% helix, 22% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, H, B, G, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1166 | 0.83 | 0.84 | 107 | ZN |
| 2 | 881 | 0.83 | 0.85 | 75 | ZN |
| 3 | 675 | 0.83 | 0.87 | 77 | ZN |
| 4 | 825 | 0.82 | 0.85 | 71 | ZN |
| 5 | 754 | 0.80 | 0.84 | 84 | NAG |
Interfaces
13 interfaces between chains.
- D–H · 1059 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 1042 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 1034 Ų buried · 22 hydrogen bonds · protein-protein
- C–G · 942 Ų buried · 22 hydrogen bonds · protein-protein
- A–G · 709 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide, 24 glycan (disulfide, N-glycosylation).
Compared structures
- 7RPV · Crystal structure of affinity-enhancing and catalytically inactive ACE2 in complex with… · the same entry in another collection · chain E against E, TM-score 1.00
- Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain C 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 7RPV · PDBe 7RPV · UniProt Q9BYF1 · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.