MolNFT v1 · #139471 · protein
Structure of the S1 subunit C-terminal domain from bat-derived coronavirus HKU5 spike protein
5XGR · Spike protein S1: “Structure of the S1 subunit C-terminal domain from bat-derived coronavirus HKU5 spike protein”. X-ray diffraction, 1 ligand (NAG), 18 pockets (best druggability 0.83). MolNFT v1 #139471 on GenesisL1: 3D structure…
- PDB
- 5XGR
- Type
- protein
- Length
- 1,584 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1
- UniProt
- A3EXD0
- Ligands
- NAG
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Spike protein S1 | protein | 198 | 17% helix, 37% strand | A3EXD0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains C, D, E, F, G, H, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.83 | 0.84 | 75 | empty |
| 2 | 947 | 0.83 | 0.84 | 81 | empty |
| 3 | 866 | 0.82 | 0.85 | 77 | empty |
| 4 | 1192 | 0.81 | 0.83 | 105 | empty |
| 5 | 358 | 0.71 | 0.83 | 71 | empty |
Interfaces
10 interfaces between chains.
- A–C · 688 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 672 Ų buried · 10 hydrogen bonds · protein-protein
- C–G · 641 Ų buried · 4 hydrogen bonds · protein-protein
- D–H · 634 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 605 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 5XGR · Structure of the S1 subunit C-terminal domain from bat-derived coronavirus HKU5 spike… · the same entry in another collection · chain D against D, 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 A3EXD0
- Elsewhere: RCSB PDB 5XGR · PDBe 5XGR · UniProt A3EXD0
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