MolNFT v1 · #180011 · protein
Cryo-EM structure of SARS-cov-2 spike in complex with Fab 15033-7, three rbds bound
7KML · Spike glycoprotein: “Cryo-EM structure of SARS-cov-2 spike in complex with Fab 15033-7, three rbds bound”. Electron microscopy, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.84). MolNFT v1 #180011 on GenesisL1: 3D structure…
- PDB
- 7KML
- Type
- protein
- Length
- 4,413 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Fab 15033-7 light chain; Fab 15033-7 heavy chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 17% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1034 | 22% helix, 35% strand | P0DTC2 |
| L, M, N | Fab 15033-7 light chain | protein | 214 | 5% helix, 51% strand | — |
| H, I, J | Fab 15033-7 heavy chain | protein | 223 | 8% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 72 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 6 copies
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 | 913 | 0.84 | 0.86 | 75 | empty |
| 2 | 622 | 0.82 | 0.87 | 86 | empty |
| 3 | 655 | 0.80 | 0.85 | 65 | empty |
| 4 | 147 | 0.79 | 0.96 | 24 | empty |
| 5 | 392 | 0.75 | 0.85 | 33 | empty |
Interfaces
12 interfaces between chains.
- B–C · 4439 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 4432 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 4429 Ų buried · 43 hydrogen bonds · protein-protein
- N–J · 1875 Ų buried · 17 hydrogen bonds · protein-protein
- M–I · 1872 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 57 disulfide, 45 glycan (disulfide, N-glycosylation).
Compared structures
- 7KML · cryo-EM structure of SARS-CoV-2 spike in complex with Fab 15033-7, three RBDs bound · 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 7KML · PDBe 7KML · UniProt P0DTC2
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