MolNFT v1 · #191344 · protein
SARS-cov-2 receptor binding domain in complex with AZ090 Fab
8DAD · AZ090 Fab heavy chain: “SARS-cov-2 receptor binding domain in complex with AZ090 Fab”. Electron microscopy, 1 ligand (NAG), 4 pockets (best druggability 0.70). MolNFT v1 #191344 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 8DAD
- Type
- protein
- Length
- 424 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AZ090 Fab heavy chain; AZ090 Fab light chain; Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.70
Structure
electron microscopy · 3 distinct chains · 9% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | AZ090 Fab heavy chain | protein | 123 | 2% helix, 50% strand | — |
| L | AZ090 Fab light chain | protein | 107 | 6% helix, 46% strand | — |
| B | Spike glycoprotein | protein | 194 | 15% helix, 27% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains H, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.70 | 0.98 | 18 | empty |
| 2 | 79 | 0.43 | 0.80 | 15 | empty |
| 3 | 115 | 0.38 | 0.74 | 25 | empty |
| 4 | 71 | 0.37 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 848 Ų buried · 6 hydrogen bonds · protein-protein
- H–B · 630 Ų buried · 9 hydrogen bonds · protein-protein
- L–B · 301 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 8DAD · SARS-CoV-2 receptor binding domain in complex with AZ090 Fab · the same entry in another collection · chain H against H, 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
- Elsewhere: RCSB PDB 8DAD · PDBe 8DAD · UniProt P0DTC2
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