Research workbench
Structure of the SARS-cov-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, BG7-15
Analyse Structure of the SARS-cov-2 S 6P trimer in complex with the human neutralizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M6G
- Type
- protein
- Length
- 3,380 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; BG7-15 Fab heavy chain; BG7-15 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 968 | 23% helix, 31% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 981 | 22% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 985 | 22% helix, 31% strand | P0DTC2 |
| H, R | BG7-15 Fab heavy chain | protein | 116 | 3% helix, 46% strand | — |
| L, S | BG7-15 Fab light chain | protein | 107 | 3% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 48 copies · chains A, C, B
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 | 1102 | 0.86 | 0.87 | 144 | empty |
| 2 | 664 | 0.83 | 0.88 | 73 | empty |
| 3 | 560 | 0.81 | 0.87 | 51 | empty |
| 4 | 409 | 0.81 | 0.89 | 62 | empty |
| 5 | 595 | 0.75 | 0.82 | 54 | empty |
Interfaces
11 interfaces between chains.
- B–C · 5170 Ų buried · 51 hydrogen bonds · protein-protein
- A–C · 4988 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 4724 Ų buried · 41 hydrogen bonds · protein-protein
- H–L · 713 Ų buried · 10 hydrogen bonds · protein-protein
- R–S · 694 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide, 36 glycan (disulfide, N-glycosylation).
Compared structures
- 7M6G · Structure of the SARS-CoV-2 S 6P 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 7M6G · PDBe 7M6G · UniProt P0DTC2
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