MolNFT v1 · #183049 · protein
EM structure of SARS-cov-2 spike glycoprotein (all rbd down) in complex with covox-253H55L Fab
7NDA: “EM structure of SARS-cov-2 spike glycoprotein (all rbd down) in complex with covox-253H55L Fab”. Electron microscopy, 2 ligands (NAG, FUC), 20 pockets (best druggability 0.82). MolNFT v1 #183049 on GenesisL1: 3D structure, binding…
- PDB
- 7NDA
- Type
- protein
- Length
- 3,452 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Covox-253H55L Fab heavy chain; Covox-253H55L Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 20% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1005 | 21% helix, 33% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1003 | 22% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1012 | 22% helix, 32% strand | P0DTC2 |
| H | Covox-253H55L Fab heavy chain | protein | 218 | 9% helix, 50% strand | — |
| L | Covox-253H55L Fab light chain | protein | 214 | 7% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 62 copies · chains A, C, B, H
- FUC · alpha-L-fucopyranose · sugar · chains H
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 | 613 | 0.82 | 0.87 | 78 | empty |
| 2 | 524 | 0.81 | 0.87 | 48 | empty |
| 3 | 294 | 0.80 | 0.92 | 34 | empty |
| 4 | 893 | 0.79 | 0.82 | 100 | empty |
| 5 | 241 | 0.78 | 0.91 | 32 | empty |
Interfaces
7 interfaces between chains.
- A–B · 5721 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 5561 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 5515 Ų buried · 44 hydrogen bonds · protein-protein
- H–L · 1790 Ų buried · 13 hydrogen bonds · protein-protein
- C–H · 622 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 47 glycan, 44 disulfide (N-glycosylation, disulfide).
Compared structures
- 7NDA · EM structure of SARS-CoV-2 Spike glycoprotein (all RBD down) in complex with… · 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 7NDA · PDBe 7NDA · UniProt P0DTC2
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