Research workbench
Cryo-EM structure of machupo virus dimeric L-Z complex
Analyse Cryo-EM structure of machupo virus dimeric L-Z complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VH1
- Type
- protein
- Length
- 1,661 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase L; MALTOSE/MALTODEXTRIN-binding periplasmic PROTEIN,RING…
- EC
- 2.7.7.48, 3.1.-.-
- UniProt
- Q6IUF8, Q6IUF9
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 38% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase L (EC 2.7.7.48, 3.1.-.-) | protein | 1612 | 39% helix, 6% strand | Q6IUF8 |
| B | MALTOSE/MALTODEXTRIN-binding periplasmic PROTEIN,RING finger protein Z | protein | 49 | 16% helix, 4% strand | Q6IUF9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.82 | 0.83 | 75 | empty |
| 2 | 284 | 0.77 | 0.89 | 53 | empty |
| 3 | 662 | 0.76 | 0.81 | 52 | empty |
| 4 | 55 | 0.73 | 0.98 | 18 | empty |
| 5 | 612 | 0.72 | 0.80 | 57 | empty |
Interfaces
1 interface between chains.
- A–B · 944 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7VH1 · Cryo-EM structure of Machupo virus dimeric L-Z complex · 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 Q6IUF8
- Every structure of UniProt Q6IUF9
- Elsewhere: RCSB PDB 7VH1 · PDBe 7VH1 · UniProt Q6IUF8 · UniProt Q6IUF9
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