MolNFT v1 · #167433 · protein
Crystal structure of stabilized gp from makona variant of ebola virus
6VKM · Virion spike glycoprotein: “Crystal structure of stabilized gp from makona variant of ebola virus”. X-ray diffraction, 1 ligand (NAG), 4 pockets (best druggability 0.66). MolNFT v1 #167433 on GenesisL1: 3D structure, binding sites…
- PDB
- 6VKM
- Type
- protein
- Length
- 353 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Virion spike glycoprotein
- UniProt
- A0A2I4PEY8, A0A0E3XL33
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Virion spike glycoprotein | protein | 353 | 21% helix, 29% strand | A0A2I4PEY8, A0A0E3XL33 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.66 | 0.95 | 18 | empty |
| 2 | 139 | 0.60 | 0.84 | 24 | empty |
| 3 | 93 | 0.38 | 0.76 | 20 | empty |
| 4 | 77 | 0.36 | 0.76 | 17 | empty |
Modifications
Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6VKM · Crystal Structure of Stabilized GP from Makona Variant of Ebola Virus · 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 A0A2I4PEY8
- Every structure of UniProt A0A0E3XL33
- Elsewhere: RCSB PDB 6VKM · PDBe 6VKM · UniProt A0A2I4PEY8 · UniProt A0A0E3XL33
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