MolNFT v1 · #177195 · protein
Immune complex of SARS-cov-2 rbd and cross-neutralizing antibody 6D6
7EAN · Spike protein S1: “Immune complex of SARS-cov-2 rbd and cross-neutralizing antibody 6D6”. X-ray diffraction, 1 ligand (NAG), 7 pockets (best druggability 0.66). MolNFT v1 #177195 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7EAN
- Type
- protein
- Length
- 627 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Heavy chain of SARS-cov-2 cross-neutralizing mab 6D6; Light chain of…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 195 | 19% helix, 30% strand | P0DTC2 |
| H | Heavy chain of SARS-cov-2 cross-neutralizing mab 6D6 | protein | 222 | 7% helix, 50% strand | — |
| L | Light chain of SARS-cov-2 cross-neutralizing mab 6D6 | protein | 210 | 7% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.66 | 0.81 | 45 | empty |
| 2 | 428 | 0.66 | 0.79 | 49 | empty |
| 3 | 710 | 0.64 | 0.74 | 61 | empty |
| 4 | 69 | 0.56 | 0.88 | 23 | empty |
| 5 | 98 | 0.38 | 0.75 | 21 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1863 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 603 Ų buried · 16 hydrogen bonds · protein-protein
- A–L · 484 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7EAN · immune complex of SARS-CoV-2 RBD and cross-neutralizing antibody 6D6 · 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 7EAN · PDBe 7EAN · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.