Research workbench
Structure of SARS-cov-2 spike at pH 5.5, single rbd up, conformation 1
Analyse Structure of SARS-cov-2 spike at pH 5.5, single rbd up, conformation 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XM3
- Type
- protein
- Length
- 3,143 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 20% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1038 | 22% helix, 30% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1058 | 19% helix, 28% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1047 | 20% helix, 29% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 60 copies · chains A, C, B
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 | 957 | 0.86 | 0.88 | 115 | empty |
| 2 | 1076 | 0.84 | 0.85 | 116 | empty |
| 3 | 1058 | 0.82 | 0.83 | 104 | empty |
| 4 | 442 | 0.81 | 0.89 | 54 | empty |
| 5 | 661 | 0.81 | 0.85 | 69 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5440 Ų buried · 46 hydrogen bonds · protein-protein
- A–C · 5401 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 4624 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 43 glycan, 41 disulfide (N-glycosylation, disulfide).
Compared structures
- 6XM3 · Structure of SARS-CoV-2 spike at pH 5.5, single RBD up, conformation 1 · 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 6XM3 · PDBe 6XM3 · UniProt P0DTC2
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