MolNFT v1 · #178712 · protein
Crystal structure of neuropilin-1 B1 domain in complex with SARS-cov-2 S1 C-end rule (cendr) peptide
7JJC: “Crystal structure of neuropilin-1 B1 domain in complex with SARS-cov-2 S1 C-end rule (cendr) peptide”. X-ray diffraction, 5 pockets (best druggability 0.82). MolNFT v1 #178712 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7JJC
- Type
- protein
- Length
- 666 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuropilin-1; Spike protein S1
- UniProt
- O14786, P0DTC2
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Neuropilin-1 | protein | 159 | 6% helix, 50% strand | O14786 |
| B, D | Neuropilin-1 | protein | 166 | 7% helix, 46% strand | O14786 |
| E, F, H | Spike protein S1 | protein | 3 | 0% helix, 0% strand | P0DTC2 |
| G | Spike protein S1 | protein | 7 | 0% helix, 0% strand | P0DTC2 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, C, B, D
- GOL · Glycerol · additive · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.82 | 0.89 | 51 | PEG |
| 2 | 201 | 0.75 | 0.90 | 37 | PEG, GOL |
| 3 | 90 | 0.33 | 0.73 | 19 | empty |
| 4 | 72 | 0.29 | 0.73 | 23 | PEG |
| 5 | 51 | 0.23 | 0.72 | 14 | empty |
Interfaces
10 interfaces between chains.
- C–D · 957 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 951 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 652 Ų buried · 4 hydrogen bonds · protein-protein
- C–G · 371 Ų buried · 9 hydrogen bonds · protein-protein
- D–H · 315 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7JJC · Crystal structure of neuropilin-1 b1 domain in complex with SARS-CoV-2 S1 C-end rule… · the same entry in another collection · chain H against H, TM-score 1.00
- O14786 · AlphaFold monomer V2.0 prediction for neuropilin-1 (O14786) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O14786
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7JJC · PDBe 7JJC · UniProt O14786 · UniProt P0DTC2
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