MolNFT v1 · #183047 · protein
EM structure of SARS-cov-2 spike glycoprotein in complex with covox- 384 Fab
7ND8: “EM structure of SARS-cov-2 spike glycoprotein in complex with covox- 384 Fab”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.85). MolNFT v1 #183047 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7ND8
- Type
- protein
- Length
- 3,447 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Covox-384 Fab heavy chain; Covox-384 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 17% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1002 | 22% helix, 33% strand | P0DTC2 |
| H | Covox-384 Fab heavy chain | protein | 228 | 7% helix, 49% strand | — |
| L | Covox-384 Fab light chain | protein | 213 | 7% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 60 copies · chains A, C, B
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 | 897 | 0.85 | 0.87 | 108 | empty |
| 2 | 636 | 0.85 | 0.90 | 83 | empty |
| 3 | 1073 | 0.80 | 0.82 | 117 | empty |
| 4 | 337 | 0.79 | 0.90 | 44 | empty |
| 5 | 375 | 0.78 | 0.87 | 51 | empty |
Interfaces
7 interfaces between chains.
- A–B · 5513 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 5509 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 5206 Ų buried · 39 hydrogen bonds · protein-protein
- H–L · 1930 Ų buried · 12 hydrogen bonds · protein-protein
- B–H · 473 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 glycan, 43 disulfide (N-glycosylation, disulfide).
Compared structures
- 7ND8 · EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-384 Fab · the same entry in another collection · chain A against A, 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 7ND8 · PDBe 7ND8 · UniProt P0DTC2
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