MolNFT v1 · #182839 · protein
SARS-cov-2 spike (2P) in complex with G32R7 Fab (rbd and ntd local reconstruction)
7N64 · Spike glycoprotein: “SARS-cov-2 spike (2P) in complex with G32R7 Fab (rbd and ntd local reconstruction)”. Electron microscopy, 2 ligands (NAG, BMA), 9 pockets (best druggability 0.72). MolNFT v1 #182839 on GenesisL1: 3D structure…
- PDB
- 7N64
- Type
- protein
- Length
- 906 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; G32R7 Fab heavy chain; G32R7 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 9 · best druggability 0.72
Structure
electron microscopy · 4 distinct chains · 5% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 277 | 0% helix, 37% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 198 | 13% helix, 27% strand | P0DTC2 |
| H | G32R7 Fab heavy chain | protein | 222 | 3% helix, 35% strand | — |
| L | G32R7 Fab light chain | protein | 209 | 4% helix, 38% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, H
- BMA · beta-D-mannopyranose · sugar
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 | 688 | 0.72 | 0.79 | 69 | empty |
| 2 | 279 | 0.68 | 0.83 | 42 | empty |
| 3 | 53 | 0.56 | 0.89 | 18 | empty |
| 4 | 369 | 0.55 | 0.74 | 60 | empty |
| 5 | 119 | 0.45 | 0.78 | 17 | empty |
Interfaces
6 interfaces between chains.
- H–L · 1818 Ų buried · 16 hydrogen bonds · protein-protein
- B–H · 1193 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 223 Ų buried · 0 hydrogen bonds · protein-protein
- A–H · 219 Ų buried · 2 hydrogen bonds · protein-protein
- B–L · 22 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7N64 · SARS-CoV-2 Spike (2P) in complex with G32R7 Fab (RBD and NTD local reconstruction) · 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 7N64 · PDBe 7N64 · UniProt P0DTC2
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