MolNFT v1 · #189091 · protein
XG005-bound SARS-cov-2 S
7V26 · Spike glycoprotein: “XG005-bound SARS-cov-2 S”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.86). MolNFT v1 #189091 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7V26
- Type
- protein
- Length
- 4,506 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; XG005 heavy chain; XG005 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 13% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Spike glycoprotein | protein | 1076 | 18% helix, 27% strand | P0DTC2 |
| a, c, e | XG005 heavy chain | protein | 223 | 0% helix, 31% strand | — |
| b, d, f | XG005 light chain | protein | 203 | 0% helix, 20% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 45 copies · chains A, C, E
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 | 773 | 0.86 | 0.89 | 100 | empty |
| 2 | 793 | 0.81 | 0.84 | 72 | empty |
| 3 | 324 | 0.77 | 0.88 | 48 | empty |
| 4 | 402 | 0.77 | 0.86 | 50 | empty |
| 5 | 613 | 0.77 | 0.83 | 48 | empty |
Interfaces
13 interfaces between chains.
- A–C · 5106 Ų buried · 44 hydrogen bonds · protein-protein
- A–E · 4612 Ų buried · 35 hydrogen bonds · protein-protein
- C–E · 4550 Ų buried · 47 hydrogen bonds · protein-protein
- c–d · 2234 Ų buried · 15 hydrogen bonds · protein-protein
- e–f · 2167 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 disulfide, 45 glycan (disulfide, N-glycosylation).
Compared structures
- 7V26 · XG005-bound SARS-CoV-2 S · 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 7V26 · PDBe 7V26 · UniProt P0DTC2
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