Research workbench
The structure of FC08 Fab-HA.CE2-rbd complex
Analyse The structure of FC08 Fab-HA.CE2-rbd complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DX4
- Type
- protein
- Length
- 1,027 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Angiotensin-converting enzyme 2; Spike protein S1; Heavy chain of FC08 Fab; Light chain…
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- Q9BYF1, P0DTC2
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.81
Structure
electron microscopy · 4 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 597 | 59% helix, 3% strand | Q9BYF1 |
| E | Spike protein S1 | protein | 194 | 11% helix, 28% strand | P0DTC2 |
| H | Heavy chain of FC08 Fab | protein | 124 | 0% helix, 39% strand | — |
| L | Light chain of FC08 Fab | protein | 112 | 3% helix, 41% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.81 | 0.92 | 40 | empty |
| 2 | 765 | 0.73 | 0.79 | 78 | empty |
| 3 | 399 | 0.66 | 0.80 | 55 | empty |
| 4 | 432 | 0.65 | 0.78 | 55 | empty |
| 5 | 59 | 0.47 | 0.85 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–E · 941 Ų buried · 11 hydrogen bonds · protein-protein
- H–L · 938 Ų buried · 15 hydrogen bonds · protein-protein
- E–H · 706 Ų buried · 7 hydrogen bonds · protein-protein
- E–L · 405 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 7DX4 · The structure of FC08 Fab-hA.CE2-RBD complex · the same entry in another collection · chain E against E, TM-score 1.00
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A 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 A 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 A 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 A 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 A 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 A 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 A 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 Q9BYF1
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7DX4 · PDBe 7DX4 · UniProt Q9BYF1 · UniProt P0DTC2
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