MolNFT v1 · #185711 · protein
Beta-06 Fab in complex with SARS-cov-2 beta-spike glycoprotein
7Q9P: “Beta-06 Fab in complex with SARS-cov-2 beta-spike glycoprotein”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.84). MolNFT v1 #185711 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7Q9P
- Type
- protein
- Length
- 3,807 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Beta-06 heavy chain; Beta-06 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Spike glycoprotein | protein | 1040 | 22% helix, 35% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1036 | 23% helix, 35% strand | P0DTC2 |
| A | Spike glycoprotein | protein | 1041 | 23% helix, 34% strand | P0DTC2 |
| H, E, J | Beta-06 heavy chain | protein | 122 | 2% helix, 49% strand | — |
| L, F, K | Beta-06 light chain | protein | 108 | 3% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 52 copies · chains B, C, A
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 | 1033 | 0.84 | 0.85 | 106 | empty |
| 2 | 529 | 0.84 | 0.90 | 74 | empty |
| 3 | 1197 | 0.80 | 0.81 | 107 | empty |
| 4 | 592 | 0.72 | 0.80 | 52 | empty |
| 5 | 240 | 0.70 | 0.86 | 27 | empty |
Interfaces
13 interfaces between chains.
- C–A · 4242 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 3821 Ų buried · 18 hydrogen bonds · protein-protein
- B–A · 3630 Ų buried · 21 hydrogen bonds · protein-protein
- H–L · 1057 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 1055 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 40 glycan (disulfide, N-glycosylation).
Compared structures
- 7Q9P · Beta-06 fab in complex with SARS-CoV-2 beta-Spike glycoprotein · the same entry in another collection · chain B against B, 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 7Q9P · PDBe 7Q9P · UniProt P0DTC2
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