MolNFT v1 · #187248 · protein
J08 fragment antigen binding in complex with SARS-cov-2-6P-MUT7 S protein (conformation 3)
7S6L · Spike glycoprotein: “J08 fragment antigen binding in complex with SARS-cov-2-6P-MUT7 S protein (conformation 3)”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.88). MolNFT v1 #187248 on GenesisL1: 3D…
- PDB
- 7S6L
- Type
- protein
- Length
- 3,117 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; J08 fragment antigen binding heavy chain variable domain; J08…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 5 distinct chains · 22% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 984 | 23% helix, 34% strand | P0DTC2 |
| H | J08 fragment antigen binding heavy chain variable domain | protein | 122 | 7% helix, 48% strand | — |
| L | J08 fragment antigen binding light chain variable domain | protein | 101 | 3% helix, 46% strand | — |
| B | Spike glycoprotein | protein | 949 | 24% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 961 | 24% helix, 34% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, B, C
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 | 955 | 0.88 | 0.89 | 107 | empty |
| 2 | 1089 | 0.83 | 0.84 | 95 | empty |
| 3 | 543 | 0.78 | 0.85 | 47 | empty |
| 4 | 831 | 0.78 | 0.81 | 84 | empty |
| 5 | 83 | 0.73 | 0.95 | 20 | empty |
Interfaces
6 interfaces between chains.
- B–C · 4667 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 4453 Ų buried · 52 hydrogen bonds · protein-protein
- A–C · 4178 Ų buried · 38 hydrogen bonds · protein-protein
- H–L · 751 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 516 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide, 23 glycan (disulfide, N-glycosylation).
Compared structures
- 7S6L · J08 fragment antigen binding in complex with SARS-CoV-2-6P-Mut7 S protein (conformation 3) · 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 7S6L · PDBe 7S6L · UniProt P0DTC2
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