MolNFT v1 · #179581 · protein
Crystal structure of SARS-cov-2 receptor binding domain in complex with the Fab fragments of neutralizing antibodies 298 and 52
7K9Z · 52 Fab heavy chain: “Crystal structure of SARS-cov-2 receptor binding domain in complex with the Fab fragments of neutralizing…”. X-ray diffraction, 1 ligand (NAG), 15 pockets (best druggability 0.69). MolNFT v1 #179581 on…
- PDB
- 7K9Z
- Type
- protein
- Length
- 1,057 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 52 Fab heavy chain; 52 Fab light chain; 298 Fab light chain; 298 Fab heavy chain; Spike…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 15 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | 52 Fab heavy chain | protein | 212 | 3% helix, 50% strand | — |
| L | 52 Fab light chain | protein | 212 | 6% helix, 43% strand | — |
| A | 298 Fab light chain | protein | 220 | 5% helix, 49% strand | — |
| B | 298 Fab heavy chain | protein | 218 | 3% helix, 47% strand | — |
| E | Spike protein S1 | protein | 195 | 14% helix, 27% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.69 | 0.98 | 18 | empty |
| 2 | 486 | 0.69 | 0.79 | 48 | empty |
| 3 | 448 | 0.62 | 0.76 | 56 | empty |
| 4 | 371 | 0.55 | 0.74 | 48 | empty |
| 5 | 334 | 0.53 | 0.74 | 44 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1932 Ų buried · 9 hydrogen bonds · protein-protein
- H–L · 1760 Ų buried · 14 hydrogen bonds · protein-protein
- H–E · 652 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 442 Ų buried · 5 hydrogen bonds · protein-protein
- L–E · 371 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7K9Z · Crystal structure of SARS-CoV-2 receptor binding domain in complex with the Fab fragments… · the same entry in another collection · chain H against H, 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 7K9Z · PDBe 7K9Z · UniProt P0DTC2
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