Research workbench
Trypsin-digested S protein of SARS-cov-2 bound with pd of ACE2 in the conformation 3 (3 up rbd and 2 pd bound)
Analyse Trypsin-digested S protein of SARS-cov-2 bound with pd of ACE2 in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DX9
- Type
- protein
- Length
- 4,209 residues
- Chains
- 5
- 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 · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spike glycoprotein | protein | 1006 | 20% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1007 | 21% helix, 32% strand | P0DTC2 |
| D, E | 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 · 93 copies · chains A, B, C, D, E
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 | 898 | 0.86 | 0.88 | 121 | empty |
| 2 | 904 | 0.83 | 0.85 | 101 | empty |
| 3 | 621 | 0.82 | 0.87 | 67 | empty |
| 4 | 1134 | 0.79 | 0.80 | 99 | empty |
| 5 | 650 | 0.74 | 0.80 | 42 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4170 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 4087 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 3968 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 901 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 893 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 glycan, 44 disulfide (N-glycosylation, disulfide).
Compared structures
- 7DX9 · Trypsin-digested S protein of SARS-CoV-2 bound with PD of ACE2 in the conformation 3 (3… · 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 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 7DX9 · PDBe 7DX9 · UniProt P0DTC2 · UniProt Q9BYF1
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