MolNFT v1 · #179565 · protein
SARS-cov-2 spike in complex with neutralizing Fab 2H04 (three down conformation)
7K9J: “SARS-cov-2 spike in complex with neutralizing Fab 2H04 (three down conformation)”. Electron microscopy, 4 ligands (NAG, BMA, FUC). MolNFT v1 #179565 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7K9J
- Type
- protein
- Length
- 3,627 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, FUC, MAN
Structure
electron microscopy · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | — | protein | 982 | — | P0DTC2 |
| H, I, J | — | protein | 121 | — | — |
| L, M, N | — | protein | 106 | — | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 84 copies · chains A, C, H, B, I, J
- BMA · beta-D-mannopyranose · sugar · 18 copies · chains C, H, I, B, J
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains H, L, A, I, M, B, J, N, C
- MAN · alpha-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 7K9J · SARS-CoV-2 Spike in complex with neutralizing Fab 2H04 (three down conformation) · 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 7K9J · PDBe 7K9J · UniProt P0DTC2
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