MolNFT v1 · #186645 · protein
Structure of the SARS-cov-2 S 6P trimer in complex with neutralizing antibody C118 (state 1)
7RKV · Spike glycoprotein: “Structure of the SARS-cov-2 S 6P trimer in complex with neutralizing antibody C118 (state 1)”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.83). MolNFT v1 #186645 on GenesisL1: 3D…
- PDB
- 7RKV
- Type
- protein
- Length
- 4,278 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; C118 Fab heavy chain; C118 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 18% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 998 | 22% helix, 34% strand | P0DTC2 |
| D, E, G | C118 Fab heavy chain | protein | 214 | 9% helix, 51% strand | — |
| H, F, L | C118 Fab light chain | protein | 214 | 6% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 39 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 | 665 | 0.83 | 0.88 | 86 | empty |
| 2 | 512 | 0.77 | 0.84 | 65 | empty |
| 3 | 278 | 0.76 | 0.89 | 40 | empty |
| 4 | 491 | 0.75 | 0.83 | 47 | empty |
| 5 | 282 | 0.74 | 0.87 | 56 | empty |
Interfaces
13 interfaces between chains.
- B–C · 3908 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 3887 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 3885 Ų buried · 33 hydrogen bonds · protein-protein
- G–L · 1688 Ų buried · 11 hydrogen bonds · protein-protein
- D–H · 1679 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 disulfide, 39 glycan (disulfide, N-glycosylation).
Compared structures
- 7RKV · Structure of the SARS-CoV-2 S 6P trimer in complex with neutralizing antibody C118 (State… · 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 7RKV · PDBe 7RKV · UniProt P0DTC2
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