MolNFT v1 · #172430 · protein
Cryo-EM structure of the SARS-cov-2 spike protein bound to neutralizing sybodies (SB23) 2-up conformation
7A29 · Spike glycoprotein: “Cryo-EM structure of the SARS-cov-2 spike protein bound to neutralizing sybodies (SB23) 2-up conformation”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #172430 on…
- PDB
- 7A29
- Type
- protein
- Length
- 3,510 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Neutralising sybody (SB23)
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spike glycoprotein | protein | 1058 | 21% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1052 | 20% helix, 34% strand | P0DTC2 |
| D, E, F | Neutralising sybody (SB23) | protein | 114 | 8% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 61 copies · chains A, B, 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 | 905 | 0.87 | 0.89 | 101 | empty |
| 2 | 912 | 0.86 | 0.87 | 124 | empty |
| 3 | 951 | 0.81 | 0.82 | 102 | empty |
| 4 | 608 | 0.76 | 0.82 | 53 | empty |
| 5 | 1160 | 0.76 | 0.78 | 104 | empty |
Interfaces
7 interfaces between chains.
- A–C · 4960 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 4419 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 4347 Ų buried · 34 hydrogen bonds · protein-protein
- B–E · 655 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 640 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 53 glycan, 40 disulfide (N-glycosylation, disulfide).
Compared structures
- 7A29 · Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23)… · 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 7A29 · PDBe 7A29 · UniProt P0DTC2
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