MolNFT v1 · #190272 · protein
Local cryoem structure of the SARS-cov-2 S6P(B.1.1.529) in complex with BD55-3152 Fab
7WR8 · Spike protein S1: “Local cryoem structure of the SARS-cov-2 S6P(B.1.1.529) in complex with BD55-3152 Fab”. Electron microscopy, 2 ligands (NAG, FUC), 4 pockets (best druggability 0.50). MolNFT v1 #190272 on GenesisL1: 3D structure…
- PDB
- 7WR8
- Type
- protein
- Length
- 417 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; BD55-3152H; BD55-3152L
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 4 · best druggability 0.50
Structure
electron microscopy · 3 distinct chains · 7% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Spike protein S1 | protein | 187 | 12% helix, 24% strand | P0DTC2 |
| A | BD55-3152H | protein | 126 | 5% helix, 35% strand | — |
| B | BD55-3152L | protein | 104 | 0% helix, 39% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains R, A
- FUC · alpha-L-fucopyranose · sugar · chains R, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.50 | 0.75 | 34 | empty |
| 2 | 174 | 0.46 | 0.75 | 24 | NAG, FUC |
| 3 | 103 | 0.40 | 0.76 | 21 | empty |
| 4 | 74 | 0.36 | 0.76 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 887 Ų buried · 7 hydrogen bonds · protein-protein
- R–B · 516 Ų buried · 7 hydrogen bonds · protein-protein
- R–A · 490 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7WR8 · Local CryoEM structure of the SARS-CoV-2 S6P(B.1.1.529) in complex with BD55-3152 Fab · the same entry in another collection · chain R against R, 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 7WR8 · PDBe 7WR8 · UniProt P0DTC2
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