Research workbench
Locally refined region of SARS-cov-2 spike in complex with antibodies B1-182.1 and A19-61.1
Analyse Locally refined region of SARS-cov-2 spike in complex with antibodies B1-182.1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TBF
- Type
- protein
- Length
- 857 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Heavy chain of SARS-cov-2 antibody B1-182.1; Light chain of…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.67
Structure
electron microscopy · 5 distinct chains · 2% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 196 | 4% helix, 22% strand | P0DTC2 |
| H | Heavy chain of SARS-cov-2 antibody B1-182.1 | protein | 215 | 3% helix, 40% strand | — |
| L | Light chain of SARS-cov-2 antibody B1-182.1 | protein | 213 | 0% helix, 24% strand | — |
| D | Heavy chain of SARS-cov-2 antibody A19-61.1 | protein | 126 | 2% helix, 42% strand | — |
| E | Light chain of SARS-cov-2 antibody A19-61.1 | protein | 107 | 0% helix, 36% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.67 | 0.86 | 45 | empty |
| 2 | 450 | 0.58 | 0.74 | 48 | empty |
| 3 | 453 | 0.56 | 0.73 | 52 | empty |
| 4 | 64 | 0.47 | 0.84 | 21 | empty |
| 5 | 141 | 0.46 | 0.77 | 27 | empty |
Interfaces
7 interfaces between chains.
- H–L · 1502 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 813 Ų buried · 2 hydrogen bonds · protein-protein
- A–H · 501 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 447 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 370 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7TBF · Locally refined region of SARS-CoV-2 spike in complex with antibodies B1-182.1 and… · 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 7TBF · PDBe 7TBF · UniProt P0DTC2
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