MolNFT v1 · #179546 · protein
Structure of the SARS-cov-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C110
7K8V · Spike glycoprotein: “Structure of the SARS-cov-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C110”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #179546 on…
- PDB
- 7K8V
- Type
- protein
- Length
- 3,390 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; C110 Fab heavy chain; C110 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 21% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 978 | 23% helix, 29% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 973 | 21% helix, 25% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 977 | 22% helix, 30% strand | P0DTC2 |
| H, M | C110 Fab heavy chain | protein | 126 | 5% helix, 33% strand | — |
| L, N | C110 Fab light chain | protein | 105 | 0% helix, 41% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 41 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 | 956 | 0.87 | 0.88 | 116 | empty |
| 2 | 646 | 0.81 | 0.86 | 59 | empty |
| 3 | 865 | 0.80 | 0.82 | 92 | empty |
| 4 | 151 | 0.79 | 0.95 | 34 | empty |
| 5 | 813 | 0.79 | 0.82 | 85 | empty |
Interfaces
9 interfaces between chains.
- A–C · 4716 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 4605 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 4308 Ų buried · 32 hydrogen bonds · protein-protein
- M–N · 595 Ų buried · 1 hydrogen bond · protein-protein
- H–L · 488 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide, 31 glycan (disulfide, N-glycosylation).
Compared structures
- 7K8V · Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody… · 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 7K8V · PDBe 7K8V · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.