MolNFT v1 · #188008 · protein
Crystal structure of SARS-cov-2 spike protein receptor-binding domain in complex with a cross-neutralizing antibody adi-62113 Fab
7T7B · Spike protein S1: “Crystal structure of SARS-cov-2 spike protein receptor-binding domain in complex with a cross-neutralizing…”. X-ray diffraction, 2 ligands (NAG, FUC), 8 pockets (best druggability 0.59). MolNFT v1 #188008 on…
- PDB
- 7T7B
- Type
- protein
- Length
- 628 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Adi-62113 Fab heavy chain; Adi-62113 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 8 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 194 | 15% helix, 30% strand | P0DTC2 |
| H | Adi-62113 Fab heavy chain | protein | 224 | 8% helix, 51% strand | — |
| L | Adi-62113 Fab light chain | protein | 210 | 7% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- FUC · alpha-L-fucopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.59 | 0.76 | 54 | empty |
| 2 | 55 | 0.58 | 0.91 | 19 | empty |
| 3 | 326 | 0.53 | 0.74 | 36 | empty |
| 4 | 96 | 0.38 | 0.76 | 18 | empty |
| 5 | 82 | 0.34 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1744 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 766 Ų buried · 13 hydrogen bonds · protein-protein
- A–L · 185 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7T7B · Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a… · 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 7T7B · PDBe 7T7B · UniProt P0DTC2
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