MolNFT v2 · #212115 · protein
S protein of SARS-CoV-2 in complex with 3711
8HLC · Spike glycoprotein: “S protein of SARS-CoV-2 in complex with 3711”. Electron microscopy at 2.8, 2 ligands (EIC, NAG), 20 pockets (best druggability 0.86). MolNFT v2 #212115 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 8HLC
- Type
- protein
- Length
- 4,569 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Homo sapiens; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike glycoprotein; heavy chain of 3711; light chain of 3711
- UniProt
- P0DTC2
- Ligands
- EIC, NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · resolution 2.8 · 3 distinct chains · 16% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1081 | 21% helix, 33% strand | P0DTC2 |
| H, I, J | heavy chain of 3711 | protein | 228 | 5% helix, 47% strand | — |
| L, M, N | light chain of 3711 | protein | 214 | 5% helix, 43% strand | — |
Ligands and binding sites
- EIC · Linoleic acid · ligand · 3 copies · chains A, C, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 93 copies · chains A, L, C, H, B, M, I, N, J
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 | 1051 | 0.86 | 0.87 | 132 | empty |
| 2 | 258 | 0.85 | 0.96 | 32 | EIC |
| 3 | 280 | 0.84 | 0.94 | 39 | EIC |
| 4 | 277 | 0.83 | 0.94 | 38 | EIC |
| 5 | 528 | 0.82 | 0.88 | 74 | empty |
Interfaces
15 interfaces between chains.
- A–B · 6582 Ų buried · 58 hydrogen bonds · protein-protein
- A–C · 6514 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 6456 Ų buried · 46 hydrogen bonds · protein-protein
- J–N · 1835 Ų buried · 9 hydrogen bonds · protein-protein
- H–L · 1834 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 57 disulfide, 51 glycan (disulfide, N-glycosylation).
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 8HLC · PDBe 8HLC · UniProt P0DTC2
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