MolNFT v1 · #179393 · protein
SARS-cov-2 spike in complex with the S2E12 neutralizing antibody Fab fragment (local refinement of the rbd and Fab variable domains)
7K45 · S2E12 neutralizing antibody Fab fragment (heavy chain): “SARS-cov-2 spike in complex with the S2E12 neutralizing antibody Fab fragment (local refinement of the rbd…”. Electron microscopy, 1 ligand (NAG), 1 pocket (best druggability…
- PDB
- 7K45
- Type
- protein
- Length
- 419 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S2E12 neutralizing antibody Fab fragment (heavy chain); S2E12 neutralizing antibody Fab…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 1 · best druggability 0.42
Structure
electron microscopy · 3 distinct chains · 11% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | S2E12 neutralizing antibody Fab fragment (heavy chain) | protein | 122 | 10% helix, 52% strand | — |
| L | S2E12 neutralizing antibody Fab fragment (light chain) | protein | 103 | 6% helix, 44% strand | — |
| B | Spike glycoprotein | protein | 194 | 15% helix, 29% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.42 | 0.80 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–L · 802 Ų buried · 6 hydrogen bonds · protein-protein
- H–B · 481 Ų buried · 5 hydrogen bonds · protein-protein
- L–B · 246 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7K45 · SARS-CoV-2 spike in complex with the S2E12 neutralizing antibody Fab fragment (local… · 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 7K45 · PDBe 7K45 · UniProt P0DTC2
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