Research workbench
Cryo-EM structure of SARS-cov-2 spike : H11-D4 nanobody complex
Analyse Cryo-EM structure of SARS-cov-2 spike : H11-D4 nanobody complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z43
- Type
- protein
- Length
- 3,351 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Nanobody
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 987 | 22% helix, 33% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 992 | 24% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 991 | 23% helix, 33% strand | P0DTC2 |
| X, Y, Z | Nanobody | protein | 127 | 6% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 66 copies · chains A, B, C
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 | 639 | 0.86 | 0.90 | 84 | empty |
| 2 | 1168 | 0.84 | 0.85 | 122 | empty |
| 3 | 785 | 0.82 | 0.85 | 78 | empty |
| 4 | 1110 | 0.78 | 0.80 | 98 | empty |
| 5 | 493 | 0.78 | 0.86 | 76 | empty |
Interfaces
7 interfaces between chains.
- B–C · 4908 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 4769 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 4500 Ų buried · 42 hydrogen bonds · protein-protein
- A–X · 648 Ų buried · 16 hydrogen bonds · protein-protein
- C–Z · 618 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 46 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 6Z43 · Cryo-EM Structure of SARS-CoV-2 Spike : H11-D4 Nanobody 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 6Z43 · PDBe 6Z43 · UniProt P0DTC2
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