MolNFT v1 · #182227 · protein
SARS-cov-2 spike in complex with neutralizing Fab SARS2-38 (three down conformation)
7MKL · Spike glycoprotein: “SARS-cov-2 spike in complex with neutralizing Fab SARS2-38 (three down conformation)”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.85). MolNFT v1 #182227 on GenesisL1: 3D structure…
- PDB
- 7MKL
- Type
- protein
- Length
- 3,164 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; SARS2-38 fv heavy chain; SARS2-38 fv light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 20% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1002 | 22% helix, 31% strand | P0DTC2 |
| B, C | Spike glycoprotein | protein | 972 | 22% helix, 29% strand | P0DTC2 |
| H | SARS2-38 fv heavy chain | protein | 113 | 4% helix, 39% strand | — |
| L | SARS2-38 fv light chain | protein | 105 | 7% helix, 33% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 63 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 | 707 | 0.85 | 0.89 | 72 | empty |
| 2 | 921 | 0.84 | 0.85 | 99 | empty |
| 3 | 854 | 0.83 | 0.85 | 79 | empty |
| 4 | 286 | 0.78 | 0.90 | 39 | empty |
| 5 | 1087 | 0.78 | 0.80 | 113 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4961 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 4914 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 4748 Ų buried · 31 hydrogen bonds · protein-protein
- H–L · 711 Ų buried · 2 hydrogen bonds · protein-protein
- A–L · 423 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 7MKL · SARS-CoV-2 Spike in complex with neutralizing Fab SARS2-38 (three down conformation) · the same entry in another collection · chain C against C, 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 7MKL · PDBe 7MKL · UniProt P0DTC2
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