MolNFT v1 · #179241 · protein
SARS-cov-2 spike in complex with LCB1 (2RBDS open)
7JZL · Spike glycoprotein: “SARS-cov-2 spike in complex with LCB1 (2RBDS open)”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #179241 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7JZL
- Type
- protein
- Length
- 3,105 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; LCB1
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 23% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 980 | 23% helix, 34% strand | P0DTC2 |
| E, G, F | LCB1 | protein | 55 | 80% helix, 0% strand | — |
| C | Spike glycoprotein | protein | 984 | 21% helix, 34% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 976 | 22% helix, 33% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 59 copies · chains A, C, B
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 | 849 | 0.87 | 0.89 | 94 | empty |
| 2 | 862 | 0.86 | 0.88 | 115 | empty |
| 3 | 957 | 0.82 | 0.83 | 105 | empty |
| 4 | 567 | 0.79 | 0.86 | 63 | empty |
| 5 | 759 | 0.75 | 0.80 | 60 | empty |
Interfaces
7 interfaces between chains.
- A–B · 4772 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 4158 Ų buried · 34 hydrogen bonds · protein-protein
- C–B · 4007 Ų buried · 37 hydrogen bonds · protein-protein
- A–E · 388 Ų buried · 1 hydrogen bond · protein-protein
- C–G · 191 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 46 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 7JZL · SARS-CoV-2 spike in complex with LCB1 (2RBDs open) · 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 7JZL · PDBe 7JZL · UniProt P0DTC2
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