Research workbench
Structure of the SARS-cov-2 spike trimer with two rbds down in complex with the Fab fragment of human neutralizing antibody clone 6
Analyse Structure of the SARS-cov-2 spike trimer with two rbds down in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MW3
- Type
- protein
- Length
- 4,295 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab of antibody clone 6, light chain; Fab of antibody clone 6, heavy chain; Spike…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 20% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, G, E | Fab of antibody clone 6, light chain | protein | 215 | 6% helix, 50% strand | — |
| H, F, D | Fab of antibody clone 6, heavy chain | protein | 212 | 4% helix, 52% strand | — |
| C, A | Spike glycoprotein | protein | 1004 | 23% helix, 32% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1006 | 23% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 72 copies · chains C, B, A
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 | 877 | 0.87 | 0.89 | 104 | empty |
| 2 | 807 | 0.83 | 0.86 | 102 | empty |
| 3 | 821 | 0.82 | 0.84 | 81 | empty |
| 4 | 924 | 0.80 | 0.82 | 67 | empty |
| 5 | 392 | 0.76 | 0.86 | 53 | empty |
Interfaces
15 interfaces between chains.
- B–A · 4718 Ų buried · 43 hydrogen bonds · protein-protein
- C–A · 4413 Ų buried · 35 hydrogen bonds · protein-protein
- C–B · 4230 Ų buried · 32 hydrogen bonds · protein-protein
- E–D · 1674 Ų buried · 10 hydrogen bonds · protein-protein
- L–H · 1674 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 52 glycan, 51 disulfide (disulfide, N-glycosylation, glycation).
Compared structures
- 7MW3 · Structure of the SARS-CoV-2 Spike trimer with two RBDs down in complex with the Fab… · the same entry in another collection · chain L against L, 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 7MW3 · PDBe 7MW3 · UniProt P0DTC2
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