Research workbench
S protein of SARS-cov-2 bound with pd of ACE2 in the conformation 3 (2 up rbd and 1 pd bound)
Analyse S protein of SARS-cov-2 bound with pd of ACE2 in the conformation 3 (2 up rbd… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DX6
- Type
- protein
- Length
- 3,544 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Angiotensin-converting enzyme 2
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- P0DTC2, Q9BYF1
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1007 | 21% helix, 33% strand | P0DTC2 |
| B, C | Spike glycoprotein | protein | 971 | 20% helix, 32% strand | P0DTC2 |
| D | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 595 | 56% helix, 4% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 82 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 | 916 | 0.86 | 0.88 | 128 | empty |
| 2 | 603 | 0.83 | 0.88 | 81 | empty |
| 3 | 626 | 0.81 | 0.86 | 72 | empty |
| 4 | 1158 | 0.78 | 0.80 | 94 | empty |
| 5 | 721 | 0.73 | 0.79 | 45 | empty |
Interfaces
4 interfaces between chains.
- B–C · 4498 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 4250 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 4136 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 902 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 glycan, 38 disulfide (N-glycosylation, disulfide).
Compared structures
- 7DX6 · S protein of SARS-CoV-2 bound with PD of ACE2 in the conformation 3 (2 up RBD and 1 PD… · the same entry in another collection · chain B against B, 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 D 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 D 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 D 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 D 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 D 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 D 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 D against A, TM-score 0.95
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 7DX6 · PDBe 7DX6 · UniProt P0DTC2 · UniProt Q9BYF1
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