MolNFT v1 · #175519 · protein
S protein of SARS-cov-2 in complex bound with T-ACE2
7CT5 · Spike glycoprotein: “S protein of SARS-cov-2 in complex bound with T-ACE2”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.82). MolNFT v1 #175519 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7CT5
- Type
- protein
- Length
- 4,804 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Angiotensin-converting enzyme 2
- EC
- 3.4.17.23
- UniProt
- P0DTC2, Q9BYF1
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 26% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1006 | 21% helix, 31% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1007 | 20% helix, 30% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1006 | 21% helix, 28% strand | P0DTC2 |
| D, E, F | Angiotensin-converting enzyme 2 (EC 3.4.17.23) | protein | 595 | 54% helix, 4% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 104 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 | 620 | 0.82 | 0.87 | 70 | empty |
| 2 | 363 | 0.78 | 0.88 | 59 | empty |
| 3 | 85 | 0.77 | 0.98 | 31 | empty |
| 4 | 82 | 0.76 | 0.98 | 28 | empty |
| 5 | 265 | 0.75 | 0.88 | 45 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4198 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 4141 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 4008 Ų buried · 28 hydrogen bonds · protein-protein
- B–E · 885 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 884 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 66 glycan, 46 disulfide (N-glycosylation, disulfide).
Compared structures
- 7CT5 · S protein of SARS-CoV-2 in complex bound with T-ACE2 · 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 F 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 F 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 P0DTC2
- Every structure of UniProt Q9BYF1
- Elsewhere: RCSB PDB 7CT5 · PDBe 7CT5 · UniProt P0DTC2 · UniProt Q9BYF1
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