MolNFT v1 · #187077 · protein
Structure of the SARS-cov-2 S 6P trimer in complex with neutralizing antibody N-612-014
7S0D · Spike glycoprotein: “Structure of the SARS-cov-2 S 6P trimer in complex with neutralizing antibody N-612-014”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #187077 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7S0D
- Type
- protein
- Length
- 4,383 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; N-612-014 Fab heavy chain; N-612-014 light chain
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 20% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1013 | 23% helix, 32% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1033 | 22% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1026 | 21% helix, 31% strand | P0DTC2 |
| H, M, O | N-612-014 Fab heavy chain | protein | 223 | 3% helix, 39% strand | — |
| L, N, P | N-612-014 light chain | protein | 214 | 5% helix, 43% strand | — |
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 | 769 | 0.84 | 0.87 | 92 | empty |
| 2 | 1188 | 0.83 | 0.84 | 140 | empty |
| 3 | 699 | 0.83 | 0.87 | 98 | empty |
| 4 | 592 | 0.80 | 0.86 | 70 | empty |
| 5 | 175 | 0.80 | 0.95 | 39 | empty |
Interfaces
12 interfaces between chains.
- B–C · 5403 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 4789 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 4653 Ų buried · 41 hydrogen bonds · protein-protein
- M–N · 2020 Ų buried · 9 hydrogen bonds · protein-protein
- H–L · 1930 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 disulfide (disulfide).
Compared structures
- 7S0D · Structure of the SARS-CoV-2 S 6P trimer in complex with neutralizing antibody N-612-014 · 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 7S0D · PDBe 7S0D · UniProt P0DTC2
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