Research workbench
Cryo-EM structure of SARS-cov spike protein in complex with three nabs X01, X10 and X17
Analyse Cryo-EM structure of SARS-cov spike protein in complex with three nabs X01, X10… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7X7V
- Type
- protein
- Length
- 873 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- X10 light chain; X10 heavy chain; X17 light chain; X17 heavy chain; X01 light chain; X01…
- UniProt
- P59594
- Ligands
- NAG
- Pockets
- 12 · best druggability 0.63
Structure
electron microscopy · 7 distinct chains · 3% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | X10 light chain | protein | 111 | 0% helix, 43% strand | — |
| H | X10 heavy chain | protein | 121 | 2% helix, 41% strand | — |
| F | X17 light chain | protein | 107 | 0% helix, 43% strand | — |
| A | X17 heavy chain | protein | 119 | 5% helix, 43% strand | — |
| D | X01 light chain | protein | 107 | 0% helix, 38% strand | — |
| C | X01 heavy chain | protein | 119 | 3% helix, 46% strand | — |
| E | Spike protein S1 | protein | 189 | 7% helix, 22% strand | P59594 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.63 | 0.77 | 40 | empty |
| 2 | 223 | 0.60 | 0.81 | 38 | empty |
| 3 | 117 | 0.58 | 0.84 | 21 | empty |
| 4 | 268 | 0.53 | 0.76 | 30 | empty |
| 5 | 115 | 0.37 | 0.74 | 22 | empty |
Interfaces
9 interfaces between chains.
- F–A · 855 Ų buried · 6 hydrogen bonds · protein-protein
- D–C · 836 Ų buried · 10 hydrogen bonds · protein-protein
- L–H · 801 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 753 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 654 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7X7V · Cryo-EM structure of SARS-CoV spike protein in complex with three nAbs X01, X10 and X17 · the same entry in another collection · chain E against E, TM-score 1.00
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain E against E, TM-score 0.89
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain E against E, TM-score 0.89
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain E against E, TM-score 0.89
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain E against E, TM-score 0.89
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain E against E, TM-score 0.88
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 P59594
- Elsewhere: RCSB PDB 7X7V · PDBe 7X7V · UniProt P59594
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