Research workbench
SARS-cov-2 spike in complex with neutralizing nanobody MNB6
Analyse SARS-cov-2 spike in complex with neutralizing nanobody MNB6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KKL
- Type
- protein
- Length
- 3,360 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Synthetic nanobody MNB6
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 22% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Spike glycoprotein | protein | 1002 | 22% helix, 35% strand | P0DTC2 |
| B, E, F | Synthetic nanobody MNB6 | protein | 118 | 14% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 63 copies · chains A, C, B, D, E
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 | 861 | 0.87 | 0.90 | 110 | empty |
| 2 | 969 | 0.84 | 0.85 | 107 | empty |
| 3 | 1046 | 0.81 | 0.82 | 80 | empty |
| 4 | 888 | 0.81 | 0.83 | 72 | empty |
| 5 | 1049 | 0.80 | 0.82 | 81 | empty |
Interfaces
9 interfaces between chains.
- A–D · 4305 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 4295 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 4290 Ų buried · 43 hydrogen bonds · protein-protein
- C–E · 983 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 980 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 7KKL · SARS-CoV-2 Spike in complex with neutralizing nanobody mNb6 · 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 7KKL · PDBe 7KKL · UniProt P0DTC2
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