MolNFT v1 · #186900 · protein
CC6.30 fragment antigen binding in complex with SARS-cov-2-6P-MUT7 S protein (non-uniform refinement)
7RU5 · Spike glycoprotein: “CC6.30 fragment antigen binding in complex with SARS-cov-2-6P-MUT7 S protein (non-uniform refinement)”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.88). MolNFT v1 #186900 on GenesisL1…
- PDB
- 7RU5
- Type
- protein
- Length
- 3,611 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; CC6.30 Fab heavy chain fv; CC6.30 Fab kappa chain fv
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 4 distinct chains · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Spike glycoprotein | protein | 1093 | 22% helix, 34% strand | P0DTC2 |
| A, B | Spike glycoprotein | protein | 1028 | 23% helix, 34% strand | P0DTC2 |
| H, D | CC6.30 Fab heavy chain fv | protein | 124 | 5% helix, 43% strand | — |
| L, E | CC6.30 Fab kappa chain fv | protein | 107 | 4% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 40 copies · chains C, A, B
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 | 1133 | 0.88 | 0.89 | 120 | empty |
| 2 | 823 | 0.84 | 0.87 | 94 | empty |
| 3 | 874 | 0.80 | 0.82 | 96 | empty |
| 4 | 487 | 0.75 | 0.83 | 40 | empty |
| 5 | 578 | 0.74 | 0.81 | 54 | empty |
Interfaces
9 interfaces between chains.
- C–B · 4836 Ų buried · 57 hydrogen bonds · protein-protein
- C–A · 4825 Ų buried · 60 hydrogen bonds · protein-protein
- A–B · 4239 Ų buried · 40 hydrogen bonds · protein-protein
- D–E · 1186 Ų buried · 10 hydrogen bonds · protein-protein
- H–L · 1077 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 50 disulfide, 30 glycan (disulfide, N-glycosylation).
Compared structures
- 7RU5 · CC6.30 fragment antigen binding in complex with SARS-CoV-2-6P-Mut7 S protein (non-uniform… · the same entry in another collection · chain C against C, 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 7RU5 · PDBe 7RU5 · UniProt P0DTC2
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