MolNFT v1 · #190461 · protein
SARS-cov-2 rbd and NB22
7X7E · Spike protein S1: “SARS-cov-2 rbd and NB22”. X-ray diffraction, 13 pockets (best druggability 0.75). MolNFT v1 #190461 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7X7E
- Type
- protein
- Length
- 972 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; NB22
- UniProt
- P0DTC2
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, F | Spike protein S1 | protein | 194 | 19% helix, 30% strand | P0DTC2 |
| A, E, B | NB22 | protein | 130 | 7% helix, 47% strand | — |
Ligands and binding sites
- PG4 · Tetraethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 533 | 0.75 | 0.83 | 72 | empty |
| 2 | 959 | 0.72 | 0.76 | 81 | empty |
| 3 | 487 | 0.71 | 0.81 | 47 | empty |
| 4 | 563 | 0.64 | 0.76 | 51 | empty |
| 5 | 61 | 0.52 | 0.87 | 17 | empty |
Interfaces
12 interfaces between chains.
- E–F · 867 Ų buried · 18 hydrogen bonds · protein-protein
- D–A · 845 Ų buried · 11 hydrogen bonds · protein-protein
- C–B · 826 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 392 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 378 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 7X7E · SARS-CoV-2 RBD and Nb22 · the same entry in another collection · chain C against C, 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 7X7E · PDBe 7X7E · UniProt P0DTC2
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