MolNFT v1 · #177164 · protein
Cryo-EM structure of the SARS-cov-2 S-6P in complex with 35B5 FAB(1 down rbd, STATE1)
7E9N · Spike glycoprotein: “Cryo-EM structure of the SARS-cov-2 S-6P in complex with 35B5 FAB(1 down rbd, STATE1)”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #177164 on GenesisL1: 3D structure…
- PDB
- 7E9N
- Type
- protein
- Length
- 4,313 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 0.87
Structure
electron microscopy · 4 distinct chains · 18% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C | Spike glycoprotein | protein | 1002 | 20% helix, 28% strand | P0DTC2 |
| A | Spike glycoprotein | protein | 977 | 22% helix, 28% strand | P0DTC2 |
| O, X, L | Light chain of 35B5 Fab | protein | 218 | 6% helix, 43% strand | — |
| P, Y, H | Heavy chain of 35B5 Fab | protein | 226 | 5% helix, 41% 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 | 815 | 0.87 | 0.89 | 82 | empty |
| 2 | 832 | 0.86 | 0.89 | 111 | empty |
| 3 | 1056 | 0.80 | 0.82 | 94 | empty |
| 4 | 828 | 0.75 | 0.79 | 67 | empty |
| 5 | 752 | 0.75 | 0.80 | 48 | empty |
Interfaces
13 interfaces between chains.
- A–C · 4232 Ų buried · 29 hydrogen bonds · protein-protein
- B–A · 4186 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 4023 Ų buried · 23 hydrogen bonds · protein-protein
- L–H · 1685 Ų buried · 5 hydrogen bonds · protein-protein
- X–Y · 1685 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 27 glycan (disulfide, N-glycosylation).
Compared structures
- 7E9N · Cryo-EM structure of the SARS-CoV-2 S-6P in complex with 35B5 Fab(1 down RBD, state1) · 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 7E9N · PDBe 7E9N · UniProt P0DTC2
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