MolNFT v1 · #179243 · protein
SARS-cov-2 spike in complex with LCB3 (2RBDS open)
7JZN · Spike glycoprotein: “SARS-cov-2 spike in complex with LCB3 (2RBDS open)”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.83). MolNFT v1 #179243 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7JZN
- Type
- protein
- Length
- 3,132 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; LCB3
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 977 | 23% helix, 34% strand | P0DTC2 |
| E, F, G | LCB3 | protein | 64 | 86% helix, 0% strand | — |
| B | Spike glycoprotein | protein | 977 | 23% helix, 33% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 986 | 22% helix, 33% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 59 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 | 1011 | 0.83 | 0.84 | 116 | empty |
| 2 | 327 | 0.82 | 0.92 | 50 | empty |
| 3 | 995 | 0.80 | 0.82 | 80 | empty |
| 4 | 663 | 0.76 | 0.82 | 47 | empty |
| 5 | 227 | 0.75 | 0.90 | 49 | empty |
Interfaces
7 interfaces between chains.
- A–B · 4339 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 4225 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 3886 Ų buried · 29 hydrogen bonds · protein-protein
- A–E · 406 Ų buried · 1 hydrogen bond · protein-protein
- B–F · 203 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 46 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 7JZN · SARS-CoV-2 spike in complex with LCB3 (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 7JZN · PDBe 7JZN · UniProt P0DTC2
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