Research workbench
SARS-cov-2 spike (6P) in complex with 3 R1-32 fabs and 3 ACE2
Analyse SARS-cov-2 spike (6P) in complex with 3 R1-32 fabs and 3 ACE2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7YEG
- Type
- protein
- Length
- 6,306 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Angiotensin-converting enzyme 2; Heavy chain of R1-32 Fab; Light…
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- P0DTC2, Q9BYF1
- Ligands
- NAG, ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 23% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1066 | 17% helix, 27% strand | P0DTC2 |
| E, J, M | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 596 | 49% helix, 2% strand | Q9BYF1 |
| H, G, N | Heavy chain of R1-32 Fab | protein | 227 | 1% helix, 44% strand | — |
| L, I, O | Light chain of R1-32 Fab | protein | 213 | 3% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 48 copies · chains A, B, C, E, J, M
- ZN · Zinc ion · metal · 3 copies · chains E, J, M
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 | 728 | 0.84 | 0.88 | 95 | empty |
| 2 | 749 | 0.83 | 0.87 | 66 | empty |
| 3 | 268 | 0.83 | 0.94 | 27 | empty |
| 4 | 439 | 0.81 | 0.89 | 60 | empty |
| 5 | 314 | 0.81 | 0.91 | 51 | empty |
Interfaces
18 interfaces between chains.
- A–C · 4582 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 4556 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 4532 Ų buried · 40 hydrogen bonds · protein-protein
- G–I · 1920 Ų buried · 10 hydrogen bonds · protein-protein
- N–O · 1889 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 63 disulfide, 42 glycan (disulfide, N-glycosylation).
Compared structures
- 7YEG · SARS-CoV-2 Spike (6P) in complex with 3 R1-32 Fabs and 3 ACE2 · the same entry in another collection · chain N against N, TM-score 1.00
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 7YEG · PDBe 7YEG · UniProt P0DTC2 · UniProt Q9BYF1
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