MolNFT v1 · #188749 · protein
Structure of the SARS-cov-2 S 6P trimer in complex with the neutralizing antibody Fab fragment, C1520
7UAP · Spike glycoprotein: “Structure of the SARS-cov-2 S 6P trimer in complex with the neutralizing antibody Fab fragment, C1520”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.84). MolNFT v1 #188749 on GenesisL1…
- PDB
- 7UAP
- Type
- protein
- Length
- 3,957 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; C1520 Fab heavy chain; C1520 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1081 | 21% helix, 29% strand | P0DTC2 |
| H, M, O | C1520 Fab heavy chain | protein | 126 | 2% helix, 37% strand | — |
| L, N, P | C1520 Fab light chain | protein | 112 | 5% helix, 33% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 59 copies · chains A, B, M, C, O, L, N, P
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 | 1031 | 0.84 | 0.85 | 119 | empty |
| 2 | 951 | 0.84 | 0.85 | 103 | empty |
| 3 | 887 | 0.84 | 0.86 | 113 | empty |
| 4 | 691 | 0.81 | 0.85 | 70 | empty |
| 5 | 325 | 0.80 | 0.91 | 44 | empty |
Interfaces
12 interfaces between chains.
- A–B · 5753 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 5390 Ų buried · 54 hydrogen bonds · protein-protein
- B–C · 5236 Ų buried · 43 hydrogen bonds · protein-protein
- B–M · 992 Ų buried · 6 hydrogen bonds · protein-protein
- A–H · 966 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 47 glycan (disulfide, N-glycosylation).
Compared structures
- 7UAP · Structure of the SARS-CoV-2 S 6P trimer in complex with the neutralizing antibody Fab… · 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 7UAP · PDBe 7UAP · UniProt P0DTC2
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