MolNFT v1 · #182548 · protein
Structure of the SARS-cov-2 spike trimer with one rbd down in complex with the Fab fragment of human neutralizing antibody clone 2
7MW5 · Fab of antibody clone 2, light chain: “Structure of the SARS-cov-2 spike trimer with one rbd down in complex with the Fab fragment of human…”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 7MW5
- Type
- protein
- Length
- 4,242 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab of antibody clone 2, light chain; Fab of antibody clone 2, heavy chain; Spike…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 6 distinct chains · 16% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, G | Fab of antibody clone 2, light chain | protein | 215 | 6% helix, 43% strand | — |
| H, F | Fab of antibody clone 2, heavy chain | protein | 209 | 3% helix, 46% strand | — |
| C | Spike glycoprotein | protein | 1057 | 20% helix, 27% strand | P0DTC2 |
| B, A | Spike glycoprotein | protein | 1057 | 20% helix, 28% strand | P0DTC2 |
| E | Fab of antibody clone 2, light chain | protein | 110 | 3% helix, 39% strand | — |
| D | Fab of antibody clone 2, heavy chain | protein | 113 | 0% helix, 42% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 83 copies · chains C, A, 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 | 707 | 0.87 | 0.91 | 94 | empty |
| 2 | 939 | 0.86 | 0.88 | 108 | empty |
| 3 | 595 | 0.82 | 0.87 | 57 | empty |
| 4 | 1087 | 0.80 | 0.82 | 94 | empty |
| 5 | 705 | 0.75 | 0.80 | 78 | empty |
Interfaces
13 interfaces between chains.
- B–A · 4510 Ų buried · 40 hydrogen bonds · protein-protein
- C–A · 4201 Ų buried · 39 hydrogen bonds · protein-protein
- C–B · 3954 Ų buried · 31 hydrogen bonds · protein-protein
- L–H · 1648 Ų buried · 12 hydrogen bonds · protein-protein
- G–F · 1612 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 glycan, 48 disulfide (N-glycosylation, disulfide, O-glycosylation).
Compared structures
- 7MW5 · Structure of the SARS-CoV-2 Spike trimer with one RBD 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 7MW5 · PDBe 7MW5 · UniProt P0DTC2
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