MolNFT v1 · #177167 · protein
Cryo-EM structure of the SARS-cov-2 S-6P in complex with 35B5 FAB(1 out rbd, STATE3)
7E9Q · Spike glycoprotein: “Cryo-EM structure of the SARS-cov-2 S-6P in complex with 35B5 FAB(1 out rbd, STATE3)”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.88). MolNFT v1 #177167 on GenesisL1: 3D structure…
- PDB
- 7E9Q
- Type
- protein
- Length
- 4,338 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Light chain of 35B5 Fab; Heavy chain of 35B5 Fab
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 16% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | Spike glycoprotein | protein | 1002 | 21% helix, 29% strand | P0DTC2 |
| L, X, E | Light chain of 35B5 Fab | protein | 218 | 6% helix, 48% strand | — |
| H, Y, F | Heavy chain of 35B5 Fab | protein | 226 | 4% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains B, A, C
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 | 989 | 0.88 | 0.89 | 107 | empty |
| 2 | 1040 | 0.86 | 0.87 | 128 | empty |
| 3 | 1069 | 0.76 | 0.78 | 125 | empty |
| 4 | 262 | 0.75 | 0.88 | 39 | empty |
| 5 | 694 | 0.74 | 0.80 | 46 | empty |
Interfaces
13 interfaces between chains.
- A–C · 4014 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 3903 Ų buried · 21 hydrogen bonds · protein-protein
- B–A · 3865 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 2215 Ų buried · 16 hydrogen bonds · protein-protein
- X–Y · 1970 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 49 disulfide, 27 glycan (disulfide, N-glycosylation).
Compared structures
- 7E9Q · Cryo-EM structure of the SARS-CoV-2 S-6P in complex with 35B5 Fab(1 out RBD, state3) · the same entry in another collection · chain B against B, 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 7E9Q · PDBe 7E9Q · UniProt P0DTC2
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