Research workbench
Trimeric SARS-cov-2 spike ectodomain in complex with biliverdin (closed conformation)
Analyse Trimeric SARS-cov-2 spike ectodomain in complex with biliverdin (closed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NT9
- Type
- protein
- Length
- 3,261 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- BLA, NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 19% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1087 | 19% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- BLA · Biliverdine IX alpha · ligand · 3 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 84 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 | 737 | 0.87 | 0.91 | 96 | empty |
| 2 | 1149 | 0.87 | 0.88 | 141 | empty |
| 3 | 1029 | 0.83 | 0.84 | 100 | empty |
| 4 | 1003 | 0.83 | 0.84 | 99 | empty |
| 5 | 1058 | 0.82 | 0.84 | 110 | empty |
Interfaces
3 interfaces between chains.
- B–C · 4986 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 4983 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 4974 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 7NT9 · Trimeric SARS-CoV-2 spike ectodomain in complex with biliverdin (closed conformation) · 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 7NT9 · PDBe 7NT9 · UniProt P0DTC2
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