MolNFT v1 · #181824 · protein
SARS-cov-2 SPIKE:FAB 3D11 complex focused refinement
7M7B · Spike glycoprotein: “SARS-cov-2 SPIKE:FAB 3D11 complex focused refinement”. Electron microscopy, 1 ligand (NAG), 8 pockets (best druggability 0.59). MolNFT v1 #181824 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7M7B
- Type
- protein
- Length
- 635 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Antibody Fab 3D11 heavy chain; Antibody Fab 3D11 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.59
Structure
electron microscopy · 3 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 209 | 14% helix, 27% strand | P0DTC2 |
| H | Antibody Fab 3D11 heavy chain | protein | 214 | 4% helix, 51% strand | — |
| L | Antibody Fab 3D11 light chain | protein | 212 | 7% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.59 | 0.78 | 47 | empty |
| 2 | 286 | 0.53 | 0.75 | 43 | empty |
| 3 | 96 | 0.35 | 0.74 | 19 | empty |
| 4 | 56 | 0.32 | 0.77 | 13 | empty |
| 5 | 50 | 0.31 | 0.77 | 11 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1691 Ų buried · 13 hydrogen bonds · protein-protein
- A–L · 503 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 370 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7M7B · SARS-CoV-2 Spike:Fab 3D11 complex focused refinement · 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 7M7B · PDBe 7M7B · UniProt P0DTC2
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