MolNFT v1 · #88826 · protein
Crystal structure of the low pH conformation of chandipura virus glycoprotein G ectodomain
4D6W: “Crystal structure of the low pH conformation of chandipura virus glycoprotein G ectodomain”. X-ray diffraction, 2 ligands (NAG, FUC), 17 pockets (best druggability 0.85). MolNFT v1 #88826 on GenesisL1: 3D structure, binding sites…
- PDB
- 4D6W
- Type
- protein
- Length
- 1,229 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein G
- UniProt
- P13180
- Ligands
- NAG, FUC
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoprotein G | protein | 407 | 17% helix, 38% strand | P13180 |
| B | Glycoprotein G | protein | 416 | 20% helix, 38% strand | P13180 |
| C | Glycoprotein G | protein | 406 | 19% helix, 37% strand | P13180 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, C
- FUC · alpha-L-fucopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 731 | 0.85 | 0.88 | 52 | empty |
| 2 | 1060 | 0.80 | 0.81 | 93 | empty |
| 3 | 826 | 0.76 | 0.80 | 69 | empty |
| 4 | 962 | 0.75 | 0.78 | 76 | empty |
| 5 | 974 | 0.70 | 0.75 | 93 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1701 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1596 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 1543 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4D6W · Crystal Structure of the low pH conformation of Chandipura Virus glycoprotein G ectodomain · 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 P13180
- Elsewhere: RCSB PDB 4D6W · PDBe 4D6W · UniProt P13180
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