Research workbench
Structure of machupo virus L polymerase in complex with Z protein and 3'-vrna (dimeric complex)
Analyse Structure of machupo virus L polymerase in complex with Z protein and 3'-vrna… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EL9
- Type
- protein + RNA
- Length
- 3,574 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase L; Ring finger protein Z; Machupo virus 3'-vrna promoter
- EC
- 2.7.7.48, 3.1.-.-
- UniProt
- Q6IVU0, Q6UY77
- Ligands
- ZN, MN
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 3 distinct chains · 42% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | RNA-directed RNA polymerase L (EC 2.7.7.48, 3.1.-.-) | protein | 1731 | 43% helix, 11% strand | Q6IVU0 |
| B, E | Ring finger protein Z | protein | 49 | 20% helix, 8% strand | Q6UY77 |
| C, F | Machupo virus 3'-vrna promoter | rna | 7 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, D, E
- MN · Manganese (II) ion · metal · 2 copies · chains A, D
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 | 1008 | 0.80 | 0.82 | 95 | empty |
| 2 | 1011 | 0.80 | 0.81 | 90 | empty |
| 3 | 117 | 0.77 | 0.96 | 28 | empty |
| 4 | 131 | 0.76 | 0.94 | 29 | empty |
| 5 | 227 | 0.75 | 0.90 | 45 | empty |
Interfaces
5 interfaces between chains.
- A–D · 3252 Ų buried · 34 hydrogen bonds · protein-protein
- D–F · 1129 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–C · 1128 Ų buried · 19 hydrogen bonds · protein-nucleic
- D–E · 931 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 931 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7EL9 · Structure of Machupo virus L polymerase in complex with Z protein and 3'-vRNA (dimeric… · 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 7EL9 · PDBe 7EL9 · UniProt Q6IVU0 · UniProt Q6UY77
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