MolNFT v1 · #191282 · protein
Rbd of SARS-cov-2 spike protein in complex with pan-sarbecovirus nanobodies 2-10, 2-67, 2-62 and 1-25
8CYJ · Pan-sarbecovirus nanobody 2-67: “Rbd of SARS-cov-2 spike protein in complex with pan-sarbecovirus nanobodies 2-10, 2-67, 2-62 and 1-25”. Electron microscopy, 6 pockets (best druggability 0.73). MolNFT v1 #191282 on GenesisL1: 3D…
- PDB
- 8CYJ
- Type
- protein
- Length
- 701 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pan-sarbecovirus nanobody 2-67; Pan-sarbecovirus nanobody 1-25; Pan-sarbecovirus nanobody…
- UniProt
- P0DTC2
- Pockets
- 6 · best druggability 0.73
Structure
electron microscopy · 5 distinct chains · 6% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pan-sarbecovirus nanobody 2-67 | protein | 127 | 5% helix, 48% strand | — |
| B | Pan-sarbecovirus nanobody 1-25 | protein | 125 | 5% helix, 54% strand | — |
| C | Pan-sarbecovirus nanobody 2-10 | protein | 128 | 5% helix, 48% strand | — |
| D | Pan-sarbecovirus nanobody 2-62 | protein | 127 | 5% helix, 49% strand | — |
| R | Spike glycoprotein | protein | 194 | 10% helix, 22% strand | P0DTC2 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.73 | 0.96 | 27 | empty |
| 2 | 196 | 0.51 | 0.76 | 28 | empty |
| 3 | 100 | 0.47 | 0.80 | 14 | empty |
| 4 | 66 | 0.31 | 0.75 | 14 | empty |
| 5 | 69 | 0.31 | 0.75 | 17 | empty |
Interfaces
4 interfaces between chains.
- B–R · 806 Ų buried · 5 hydrogen bonds · protein-protein
- D–R · 720 Ų buried · 11 hydrogen bonds · protein-protein
- C–R · 717 Ų buried · 17 hydrogen bonds · protein-protein
- A–R · 562 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 8CYJ · RBD of SARS-CoV-2 Spike protein in complex with pan-sarbecovirus nanobodies 2-10, 2-67… · 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 8CYJ · PDBe 8CYJ · UniProt P0DTC2
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