Research workbench
Structure of rbd directed antibody DH1042 in complex with SARS-cov-2 spike: local refinement of rbd-Fab interface
Analyse Structure of rbd directed antibody DH1042 in complex with SARS-cov-2 spike… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7THE
- Type
- protein
- Length
- 423 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; DH1042 Fab heavy chain; DH1042 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 2 · best druggability 0.44
Structure
electron microscopy · 3 distinct chains · 9% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 195 | 17% helix, 29% strand | P0DTC2 |
| B | DH1042 Fab heavy chain | protein | 122 | 2% helix, 50% strand | — |
| C | DH1042 Fab light chain | protein | 106 | 3% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.44 | 0.75 | 34 | empty |
| 2 | 133 | 0.41 | 0.75 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 833 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 828 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 214 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7THE · Structure of RBD directed antibody DH1042 in complex with SARS-CoV-2 spike: Local… · 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 7THE · PDBe 7THE · UniProt P0DTC2
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