MolNFT v1 · #169485 · protein
Complex of SARS-cov-2 receptor binding domain with the Fab fragments of two neutralizing antibodies
6XDG · Spike protein S1: “Complex of SARS-cov-2 receptor binding domain with the Fab fragments of two neutralizing antibodies”. Electron microscopy, 3 ligands (NAG, BMA, MAN), 13 pockets (best druggability 0.72). MolNFT v1 #169485 on…
- PDB
- 6XDG
- Type
- protein
- Length
- 1,043 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; REGN10933 antibody Fab fragment light chain; REGN10933 antibody Fab…
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, MAN
- Pockets
- 13 · best druggability 0.72
Structure
electron microscopy · 5 distinct chains · 6% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Spike protein S1 | protein | 194 | 13% helix, 23% strand | P0DTC2 |
| D | REGN10933 antibody Fab fragment light chain | protein | 214 | 6% helix, 46% strand | — |
| B | REGN10933 antibody Fab fragment heavy chain | protein | 212 | 4% helix, 43% strand | — |
| C | REGN10987 antibody Fab fragment heavy chain | protein | 212 | 4% helix, 37% strand | — |
| A | REGN10987 antibody Fab fragment light chain | protein | 211 | 5% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.72 | 0.94 | 29 | empty |
| 2 | 102 | 0.63 | 0.89 | 37 | empty |
| 3 | 562 | 0.63 | 0.75 | 60 | empty |
| 4 | 141 | 0.61 | 0.85 | 21 | empty |
| 5 | 50 | 0.54 | 0.89 | 16 | empty |
Interfaces
6 interfaces between chains.
- C–A · 1760 Ų buried · 12 hydrogen bonds · protein-protein
- D–B · 1640 Ų buried · 11 hydrogen bonds · protein-protein
- E–B · 805 Ų buried · 11 hydrogen bonds · protein-protein
- E–C · 536 Ų buried · 6 hydrogen bonds · protein-protein
- E–D · 190 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6XDG · Complex of SARS-CoV-2 receptor binding domain with the Fab fragments of two neutralizing… · 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 6XDG · PDBe 6XDG · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.