MolNFT v1 · #188966 · protein
Crystal structure of SARS-cov-2 S delta variant receptor-binding domain (rbd) in complex COV11 Fab crystal form 2
7URS · Spike protein S1: “Crystal structure of SARS-cov-2 S delta variant receptor-binding domain (rbd) in complex COV11 Fab crystal…”. X-ray diffraction, 2 ligands (NAG, PO4), 8 pockets (best druggability 0.63). MolNFT v1 #188966 on…
- PDB
- 7URS
- Type
- protein
- Length
- 616 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; COV11 Fab heavy chain
- UniProt
- P0DTC2
- Ligands
- NAG, PO4
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 189 | 17% helix, 30% strand | P0DTC2 |
| H | COV11 Fab heavy chain | protein | 212 | 10% helix, 51% strand | — |
| L | COV11 Fab heavy chain | protein | 215 | 7% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.63 | 0.85 | 22 | MPD |
| 2 | 81 | 0.58 | 0.88 | 29 | empty |
| 3 | 168 | 0.47 | 0.76 | 32 | empty |
| 4 | 229 | 0.46 | 0.73 | 38 | empty |
| 5 | 79 | 0.33 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1709 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 893 Ų buried · 17 hydrogen bonds · protein-protein
- A–L · 438 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7URS · Crystal Structure of SARS-CoV-2 S delta variant receptor-binding domain (RBD) in complex… · 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 7URS · PDBe 7URS · UniProt P0DTC2
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