Research workbench
SARS-COV2 spike glycoprotein N-terminal heptad repeat domain + SARS- COV2(QEYKKEKE)
Analyse SARS-COV2 spike glycoprotein N-terminal heptad repeat domain + SARS… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X45
- Type
- protein
- Length
- 260 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S2'
- UniProt
- P0DTC2
- Ligands
- NH2
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F | Spike protein S2' | protein | 34 | 50% helix, 0% strand | P0DTC2 |
| D | Spike protein S2' | protein | 36 | 56% helix, 0% strand | P0DTC2 |
| C | Spike protein S2' | protein | 52 | 96% helix, 0% strand | P0DTC2 |
| B | Spike protein S2' | protein | 53 | 92% helix, 0% strand | P0DTC2 |
| A | Spike protein S2' | protein | 51 | 92% helix, 0% strand | P0DTC2 |
Ligands and binding sites
- NH2 · Amino group · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.72 | 0.98 | 16 | empty |
Interfaces
9 interfaces between chains.
- D–B · 1067 Ų buried · 15 hydrogen bonds · protein-protein
- D–A · 1056 Ų buried · 11 hydrogen bonds · protein-protein
- F–A · 983 Ų buried · 8 hydrogen bonds · protein-protein
- E–B · 964 Ų buried · 13 hydrogen bonds · protein-protein
- E–C · 957 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6X45 · SARS-CoV2 spike glycoprotein N-terminal heptad repeat domain + SARS-CoV2(QEYKKEKE) · the same entry in another collection · chain E against E, 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 6X45 · PDBe 6X45 · UniProt P0DTC2
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