Research workbench
SARS-cov-2 spike rbd in complex with neutralizing Fab SARS2-38 (local refinement)
Analyse SARS-cov-2 spike rbd in complex with neutralizing Fab SARS2-38 (local… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MKM
- Type
- protein
- Length
- 406 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; SARS2-38 fv heavy chain; SARS2-38 fv light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.71
Structure
electron microscopy · 3 distinct chains · 8% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 188 | 11% helix, 22% strand | P0DTC2 |
| H | SARS2-38 fv heavy chain | protein | 113 | 4% helix, 39% strand | — |
| L | SARS2-38 fv light chain | protein | 105 | 7% helix, 33% 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
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.71 | 0.85 | 46 | empty |
| 2 | 54 | 0.70 | 0.98 | 15 | empty |
| 3 | 221 | 0.68 | 0.85 | 28 | empty |
| 4 | 180 | 0.65 | 0.84 | 29 | empty |
| 5 | 291 | 0.59 | 0.78 | 33 | empty |
Interfaces
3 interfaces between chains.
- H–L · 720 Ų buried · 2 hydrogen bonds · protein-protein
- A–L · 430 Ų buried · 6 hydrogen bonds · protein-protein
- A–H · 164 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7MKM · SARS-CoV-2 Spike RBD in complex with neutralizing Fab SARS2-38 (local refinement) · 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 7MKM · PDBe 7MKM · UniProt P0DTC2
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