MolNFT v1 · #191407 · protein
Cryo-EM structure of SARS-cov-2 gamma (P.1) spike protein in complex with human ACE2
8DLP · Spike glycoprotein: “Cryo-EM structure of SARS-cov-2 gamma (P.1) spike protein in complex with human ACE2”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.86). MolNFT v1 #191407 on GenesisL1: 3D structure…
- PDB
- 8DLP
- Type
- protein
- Length
- 4,908 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Processed angiotensin-converting enzyme 2
- UniProt
- P0DTC2, Q9BYF1
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1040 | 21% helix, 35% strand | P0DTC2 |
| D, E, F | Processed angiotensin-converting enzyme 2 | protein | 596 | 63% helix, 4% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 78 copies · chains A, B, C, D, E, F
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 | 889 | 0.86 | 0.88 | 109 | empty |
| 2 | 408 | 0.77 | 0.87 | 57 | empty |
| 3 | 135 | 0.77 | 0.95 | 26 | empty |
| 4 | 632 | 0.75 | 0.81 | 46 | empty |
| 5 | 656 | 0.72 | 0.79 | 47 | empty |
Interfaces
6 interfaces between chains.
- B–C · 4435 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 4425 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 4395 Ų buried · 40 hydrogen bonds · protein-protein
- C–F · 905 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 900 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 glycan, 48 disulfide (N-glycosylation, disulfide).
Compared structures
- 8DLP · Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with human ACE2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain F 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 E 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 E against A, TM-score 0.99
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 P0DTC2
- Every structure of UniProt Q9BYF1
- Elsewhere: RCSB PDB 8DLP · PDBe 8DLP · UniProt P0DTC2 · UniProt Q9BYF1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.