MolNFT v1 · #185710 · protein
Beta-53 Fab in complex with SARS-cov-2 beta-spike glycoprotein
7Q9M: “Beta-53 Fab in complex with SARS-cov-2 beta-spike glycoprotein”. Electron microscopy, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.87). MolNFT v1 #185710 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7Q9M
- Type
- protein
- Length
- 3,613 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Beta-53 Fab heavy chain; Beta-53 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 976 | 23% helix, 31% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 978 | 23% helix, 30% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 975 | 23% helix, 31% strand | P0DTC2 |
| H, J, E | Beta-53 Fab heavy chain | protein | 119 | 5% helix, 50% strand | — |
| L, K, F | Beta-53 Fab light chain | protein | 109 | 0% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 41 copies · chains A, J, B, E, C, H
- BMA · beta-D-mannopyranose · sugar · 2 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 | 1129 | 0.87 | 0.88 | 130 | empty |
| 2 | 837 | 0.81 | 0.84 | 89 | empty |
| 3 | 798 | 0.81 | 0.84 | 89 | empty |
| 4 | 486 | 0.79 | 0.87 | 61 | empty |
| 5 | 444 | 0.79 | 0.87 | 49 | empty |
Interfaces
12 interfaces between chains.
- B–C · 4709 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 4497 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 4262 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 893 Ų buried · 6 hydrogen bonds · protein-protein
- J–K · 882 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 43 disulfide, 28 glycan (disulfide, N-glycosylation).
Compared structures
- 7Q9M · Beta-53 fab in complex with SARS-CoV-2 beta-Spike glycoprotein · the same entry in another collection · chain J against J, 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 7Q9M · PDBe 7Q9M · UniProt P0DTC2
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