MolNFT v1 · #126798 · protein
Structural intermediates in the fusion associated transition of vesiculovirus glycoprotein
5MDM: “Structural intermediates in the fusion associated transition of vesiculovirus glycoprotein”. X-ray diffraction, 3 ligands (NAG, FUC, SO4), 20 pockets (best druggability 0.86). MolNFT v1 #126798 on GenesisL1: 3D structure, binding…
- PDB
- 5MDM
- Type
- protein
- Length
- 1,616 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein
- UniProt
- P13180
- Ligands
- NAG, FUC, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, A | Glycoprotein | protein | 410 | 18% helix, 39% strand | P13180 |
| F, C | Glycoprotein | protein | 398 | 14% helix, 37% strand | P13180 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains F, A, C
- FUC · alpha-L-fucopyranose · sugar · chains F
- SO4 · Sulfate ion · ion · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.86 | 0.87 | 96 | empty |
| 2 | 1190 | 0.85 | 0.85 | 90 | empty |
| 3 | 423 | 0.64 | 0.78 | 57 | empty |
| 4 | 324 | 0.63 | 0.79 | 45 | empty |
| 5 | 378 | 0.63 | 0.78 | 52 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1807 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1788 Ų buried · 15 hydrogen bonds · protein-protein
- E–A · 802 Ų buried · 3 hydrogen bonds · protein-protein
- F–A · 595 Ų buried · 8 hydrogen bonds · protein-protein
- E–C · 591 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5MDM · Structural intermediates in the fusion associated transition of vesiculovirus glycoprotein · 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 P13180
- Elsewhere: RCSB PDB 5MDM · PDBe 5MDM · UniProt P13180
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