Research workbench
Trimeric SARS-cov-2 spike ectodomain in complex with biliverdin (one rbd erect)
Analyse Trimeric SARS-cov-2 spike ectodomain in complex with biliverdin (one rbd erect) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NTA
- 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 0.88
Structure
electron microscopy · 1 distinct chain · 20% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C, A | Spike glycoprotein | protein | 1087 | 20% helix, 31% strand | P0DTC2 |
Ligands and binding sites
- BLA · Biliverdine IX alpha · ligand · 3 copies · chains B, C, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 77 copies · chains B, C, A
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 | 987 | 0.88 | 0.89 | 116 | empty |
| 2 | 1020 | 0.87 | 0.88 | 119 | empty |
| 3 | 1053 | 0.85 | 0.86 | 111 | empty |
| 4 | 857 | 0.83 | 0.86 | 88 | empty |
| 5 | 674 | 0.75 | 0.81 | 45 | empty |
Interfaces
3 interfaces between chains.
- B–C · 4895 Ų buried · 38 hydrogen bonds · protein-protein
- B–A · 4772 Ų buried · 39 hydrogen bonds · protein-protein
- C–A · 4298 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 53 glycan, 42 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 7NTA · Trimeric SARS-CoV-2 spike ectodomain in complex with biliverdin (one RBD erect) · the same entry in another collection · chain B against B, 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 7NTA · PDBe 7NTA · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.