MolNFT v1 · #126123 · protein
Crystal structure of lymphocytic choriomeningitis mammarenavirus endonuclease complexed with catalytic ions
5LTF · RNA-directed RNA polymerase L: “Crystal structure of lymphocytic choriomeningitis mammarenavirus endonuclease complexed with catalytic ions”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.41). MolNFT v1 #126123 on…
- PDB
- 5LTF
- Type
- protein
- Length
- 387 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase L
- EC
- 2.7.7.48
- UniProt
- A0A059U381
- Ligands
- MG
- Pockets
- 4 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | RNA-directed RNA polymerase L (EC 2.7.7.48) | protein | 199 | 57% helix, 14% strand | A0A059U381 |
| A | RNA-directed RNA polymerase L (EC 2.7.7.48) | protein | 188 | 52% helix, 13% strand | A0A059U381 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.41 | 0.82 | 13 | empty |
| 2 | 96 | 0.39 | 0.76 | 14 | empty |
| 3 | 62 | 0.32 | 0.76 | 14 | empty |
| 4 | 61 | 0.30 | 0.75 | 19 | MG |
Interfaces
1 interface between chains.
- B–A · 663 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5LTF · Crystal structure of Lymphocytic choriomeningitis mammarenavirus endonuclease complexed… · the same entry in another collection · chain B against B, 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 A0A059U381
- Elsewhere: RCSB PDB 5LTF · PDBe 5LTF · UniProt A0A059U381
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