MolNFT v1 · #139112 · protein
Prefusion structure of MERS-cov spike glycoprotein, three-fold symmetry
5X59 · S protein: “Prefusion structure of MERS-cov spike glycoprotein, three-fold symmetry”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.86). MolNFT v1 #139112 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5X59
- Type
- protein
- Length
- 3,423 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S protein
- UniProt
- W6A028
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 20% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | S protein | protein | 1141 | 20% helix, 23% strand | W6A028 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 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 | 998 | 0.86 | 0.87 | 83 | empty |
| 2 | 317 | 0.79 | 0.90 | 79 | empty |
| 3 | 707 | 0.79 | 0.83 | 99 | empty |
| 4 | 432 | 0.78 | 0.87 | 60 | empty |
| 5 | 529 | 0.77 | 0.84 | 45 | empty |
Interfaces
3 interfaces between chains.
- B–C · 4576 Ų buried · 60 hydrogen bonds · protein-protein
- A–B · 4529 Ų buried · 56 hydrogen bonds · protein-protein
- A–C · 4503 Ų buried · 54 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 3 glycan (disulfide, glycosylation).
Compared structures
- 5X59 · Prefusion structure of MERS-CoV spike glycoprotein, three-fold symmetry · 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 W6A028
- Elsewhere: RCSB PDB 5X59 · PDBe 5X59 · UniProt W6A028
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