Research workbench
Cryo-EM structure of SARS-cov-2 spike in complex with non-neutralizing ntd-directed CV3-13 Fab isolated from convalescent individual
Analyse Cryo-EM structure of SARS-cov-2 spike in complex with non-neutralizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RQ6
- Type
- protein
- Length
- 3,951 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; CV3-13 Fab heavy chain; CV3-13 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 17% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1086 | 19% helix, 22% strand | P0DTC2 |
| H, D, J | CV3-13 Fab heavy chain | protein | 124 | 5% helix, 55% strand | — |
| L, E, K | CV3-13 Fab light chain | protein | 107 | 3% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 42 copies · chains A, B, C
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 | 1091 | 0.88 | 0.89 | 147 | empty |
| 2 | 826 | 0.83 | 0.86 | 71 | empty |
| 3 | 1138 | 0.83 | 0.84 | 121 | empty |
| 4 | 972 | 0.81 | 0.82 | 108 | empty |
| 5 | 995 | 0.80 | 0.82 | 101 | empty |
Interfaces
12 interfaces between chains.
- B–C · 4427 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 4423 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 4418 Ų buried · 33 hydrogen bonds · protein-protein
- J–K · 884 Ų buried · 5 hydrogen bonds · protein-protein
- H–L · 884 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide, 39 glycan (disulfide, N-glycosylation).
Compared structures
- 7RQ6 · Cryo-EM structure of SARS-CoV-2 spike in complex with non-neutralizing NTD-directed… · 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 7RQ6 · PDBe 7RQ6 · UniProt P0DTC2
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