MolNFT v1 · #177529 · protein
Structure of machupo virus L polymerase in complex with Z protein (dimeric form)
7ELB · RNA-directed RNA polymerase L: “Structure of machupo virus L polymerase in complex with Z protein (dimeric form)”. Electron microscopy, 2 ligands (ZN, MN), 20 pockets (best druggability 0.84). MolNFT v1 #177529 on GenesisL1: 3D…
- PDB
- 7ELB
- Type
- protein
- Length
- 3,972 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase L; Ring finger protein Z
- EC
- 2.7.7.48, 3.1.-.-
- UniProt
- Q6IVU0, Q6UY77
- Ligands
- ZN, MN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 42% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | RNA-directed RNA polymerase L (EC 2.7.7.48, 3.1.-.-) | protein | 1937 | 43% helix, 9% strand | Q6IVU0 |
| B, D | Ring finger protein Z | protein | 49 | 20% helix, 0% strand | Q6UY77 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 2 copies · chains A, 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 | 521 | 0.84 | 0.90 | 76 | empty |
| 2 | 963 | 0.83 | 0.85 | 81 | empty |
| 3 | 871 | 0.82 | 0.84 | 78 | empty |
| 4 | 253 | 0.81 | 0.93 | 40 | empty |
| 5 | 1032 | 0.81 | 0.82 | 86 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2792 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 899 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 895 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7ELB · Structure of Machupo virus L polymerase in complex with Z protein (dimeric form) · 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 Q6IVU0
- Every structure of UniProt Q6UY77
- Elsewhere: RCSB PDB 7ELB · PDBe 7ELB · UniProt Q6IVU0 · UniProt Q6UY77
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