Research workbench
Complex between the Fab arm of ab-3467 and the SARS-cov-2 receptor binding domain (rbd)
Analyse Complex between the Fab arm of ab-3467 and the SARS-cov-2 receptor binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MSQ
- Type
- protein
- Length
- 1,253 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Ab-3467 Fab heavy chain; Ab-3467 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, MAN, FUC, CL, SCN
- Pockets
- 17 · best druggability 0.62
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 195 | 16% helix, 30% strand | P0DTC2 |
| B | Spike protein S1 | protein | 189 | 16% helix, 30% strand | P0DTC2 |
| D, H | Ab-3467 Fab heavy chain | protein | 221 | 7% helix, 52% strand | — |
| E | Ab-3467 Fab light chain | protein | 213 | 6% helix, 52% strand | — |
| L | Ab-3467 Fab light chain | protein | 214 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar
- CL · Chloride ion · ion · 7 copies · chains A, B, D, E, H, L
- SCN · Thiocyanate ion · ion · 5 copies · chains B, E, L, H
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.62 | 0.74 | 50 | empty |
| 2 | 308 | 0.60 | 0.78 | 34 | empty |
| 3 | 497 | 0.59 | 0.74 | 51 | CL, GOL |
| 4 | 408 | 0.59 | 0.76 | 51 | empty |
| 5 | 72 | 0.56 | 0.88 | 19 | empty |
Interfaces
8 interfaces between chains.
- D–E · 1850 Ų buried · 12 hydrogen bonds · protein-protein
- H–L · 1830 Ų buried · 13 hydrogen bonds · protein-protein
- D–L · 695 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 669 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 643 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7MSQ · Complex between the Fab arm of AB-3467 and the SARS-CoV-2 receptor binding domain (RBD) · 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 7MSQ · PDBe 7MSQ · UniProt P0DTC2
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