MolNFT v1 · #190468 · protein
Cryo-EM structure of SARS-cov-2 delta variant spike protein in complex with three nabs X01, X10 and X17
7X7U · Spike protein S1: “Cryo-EM structure of SARS-cov-2 delta variant spike protein in complex with three nabs X01, X10 and X17”. Electron microscopy, 1 ligand (NAG), 13 pockets (best druggability 0.66). MolNFT v1 #190468 on GenesisL1…
- PDB
- 7X7U
- Type
- protein
- Length
- 878 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; X10 light chain; X10 heavy chain; X17 light chain; X17 heavy chain; X01…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 13 · best druggability 0.66
Structure
electron microscopy · 7 distinct chains · 3% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Spike protein S1 | protein | 194 | 8% helix, 21% strand | P0DTC2 |
| L | X10 light chain | protein | 111 | 0% helix, 41% strand | — |
| H | X10 heavy chain | protein | 121 | 2% helix, 43% strand | — |
| B | X17 light chain | protein | 107 | 0% helix, 38% strand | — |
| A | X17 heavy chain | protein | 119 | 3% helix, 49% strand | — |
| D | X01 light chain | protein | 107 | 0% helix, 35% strand | — |
| C | X01 heavy chain | protein | 119 | 3% helix, 42% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.66 | 0.77 | 44 | empty |
| 2 | 240 | 0.61 | 0.81 | 41 | empty |
| 3 | 214 | 0.46 | 0.74 | 38 | empty |
| 4 | 156 | 0.42 | 0.74 | 27 | empty |
| 5 | 94 | 0.40 | 0.77 | 19 | empty |
Interfaces
9 interfaces between chains.
- D–C · 904 Ų buried · 8 hydrogen bonds · protein-protein
- B–A · 846 Ų buried · 5 hydrogen bonds · protein-protein
- G–A · 839 Ų buried · 9 hydrogen bonds · protein-protein
- L–H · 835 Ų buried · 9 hydrogen bonds · protein-protein
- G–L · 637 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7X7U · Cryo-EM structure of SARS-CoV-2 Delta variant spike protein in complex with three nAbs… · the same entry in another collection · chain G against G, 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 7X7U · PDBe 7X7U · UniProt P0DTC2
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