Research workbench
Structure determination of the NB1B11-rbd complex
Analyse Structure determination of the NB1B11-rbd complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FAU
- Type
- protein
- Length
- 607 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; NB_1B11
- UniProt
- P0DTC2
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 170 | 16% helix, 29% strand | P0DTC2 |
| B, D | NB_1B11 | protein | 126 | 7% helix, 50% strand | — |
| C | Spike protein S1 | protein | 185 | 19% helix, 29% strand | P0DTC2 |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 228 | 0.55 | 0.78 | 24 | empty |
| 2 | 55 | 0.45 | 0.84 | 20 | empty |
| 3 | 126 | 0.39 | 0.74 | 25 | ZN |
| 4 | 67 | 0.37 | 0.77 | 17 | empty |
| 5 | 102 | 0.37 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 778 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 775 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 772 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7FAU · Structure Determination of the NB1B11-RBD Complex · 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 7FAU · PDBe 7FAU · UniProt P0DTC2
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