MolNFT v1 · #126131 · protein
Crystal structure of lymphocytic choriomeningitis mammarenavirus endonuclease complexed with dpba
5LTN · RNA-directed RNA polymerase L: “Crystal structure of lymphocytic choriomeningitis mammarenavirus endonuclease complexed with dpba”. X-ray diffraction, 4 ligands (XI7, MG, NA), 3 pockets (best druggability 0.43). MolNFT v1 #126131 on…
- PDB
- 5LTN
- Type
- protein
- Length
- 377 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
- XI7, MG, NA, CL
- Pockets
- 3 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase L (EC 2.7.7.48) | protein | 183 | 57% helix, 14% strand | A0A059U381 |
| B | RNA-directed RNA polymerase L (EC 2.7.7.48) | protein | 194 | 58% helix, 13% strand | A0A059U381 |
Ligands and binding sites
- XI7 · 2-4-dioxo-4-phenylbutanoic acid · ligand · chains A
- MG · Magnesium ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.43 | 0.76 | 16 | empty |
| 2 | 103 | 0.35 | 0.73 | 21 | MG |
| 3 | 84 | 0.33 | 0.74 | 19 | MG, XI7 |
Interfaces
1 interface between chains.
- A–B · 625 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5LTN · Crystal structure of Lymphocytic choriomeningitis mammarenavirus endonuclease complexed… · 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 A0A059U381
- Elsewhere: RCSB PDB 5LTN · PDBe 5LTN · UniProt A0A059U381
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