Research workbench
SARS-cov-2 S trimer with one rbd in the open state and complexed with one H014 Fab.
Analyse SARS-cov-2 S trimer with one rbd in the open state and complexed with one H014… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CAC
- Type
- protein
- Length
- 3,499 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Light chain of H014 Fab; Heavy chain of H014 Fab
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 17% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1026 | 22% helix, 28% strand | P0DTC2 |
| D | Light chain of H014 Fab | protein | 207 | 5% helix, 47% strand | — |
| E | Heavy chain of H014 Fab | protein | 214 | 3% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 60 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 574 | 0.86 | 0.92 | 88 | empty |
| 2 | 729 | 0.80 | 0.84 | 68 | empty |
| 3 | 272 | 0.80 | 0.91 | 33 | empty |
| 4 | 583 | 0.77 | 0.84 | 43 | empty |
| 5 | 407 | 0.76 | 0.86 | 56 | empty |
Interfaces
7 interfaces between chains.
- A–C · 4587 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 4526 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 4083 Ų buried · 36 hydrogen bonds · protein-protein
- D–E · 1678 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 820 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 47 glycan, 37 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 7CAC · SARS-CoV-2 S trimer with one RBD in the open state and complexed with one H014 Fab. · 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 7CAC · PDBe 7CAC · UniProt P0DTC2
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