MolNFT v1 · #183052 · protein
EM structure of SARS-cov-2 spike glycoprotein (one rbd up) in complex with covox-159
7NDD: “EM structure of SARS-cov-2 spike glycoprotein (one rbd up) in complex with covox-159”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.84). MolNFT v1 #183052 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7NDD
- Type
- protein
- Length
- 3,852 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Covox-159 Fab heavy chain; Covox-159 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1063 | 22% helix, 32% strand | P0DTC2 |
| D, F, H | Covox-159 Fab heavy chain | protein | 115 | 8% helix, 53% strand | — |
| E, G, L | Covox-159 Fab light chain | protein | 106 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 54 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 | 761 | 0.84 | 0.87 | 92 | empty |
| 2 | 748 | 0.82 | 0.85 | 87 | empty |
| 3 | 516 | 0.81 | 0.88 | 73 | empty |
| 4 | 1002 | 0.80 | 0.82 | 100 | empty |
| 5 | 744 | 0.78 | 0.82 | 75 | empty |
Interfaces
12 interfaces between chains.
- A–C · 4881 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 4826 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 4465 Ų buried · 37 hydrogen bonds · protein-protein
- H–L · 684 Ų buried · 4 hydrogen bonds · protein-protein
- F–G · 683 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 39 glycan (disulfide, N-glycosylation).
Compared structures
- 7NDD · EM structure of SARS-CoV-2 Spike glycoprotein (one RBD up) in complex with COVOX-159 · 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 7NDD · PDBe 7NDD · UniProt P0DTC2
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