Research workbench
Crystal structure of lymphocytic choriomeningitis mammarenavirus endonuclease bound to compound L742001
Analyse Crystal structure of lymphocytic choriomeningitis mammarenavirus endonuclease… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T2T
- Type
- protein
- Length
- 388 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
- A0A059U382
- Ligands
- 0N8, MN, NA, CL
- Pockets
- 3 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase L (EC 2.7.7.48) | protein | 189 | 54% helix, 13% strand | A0A059U382 |
| B | RNA-directed RNA polymerase L (EC 2.7.7.48) | protein | 199 | 56% helix, 13% strand | A0A059U382 |
Ligands and binding sites
- 0N8 · (2Z)-4-[1-benzyl-4-(4-chlorobenzyl)piperidin-4-yl]-2-hydroxy-4-oxobut-2-enoic acid · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains B
- CL · Chloride ion · ion · 2 copies · chains B
- GOL · Glycerol · additive · 2 copies · chains A, B
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 | 152 | 0.46 | 0.77 | 19 | GOL |
| 2 | 71 | 0.31 | 0.74 | 14 | empty |
| 3 | 59 | 0.28 | 0.74 | 19 | MN |
Interfaces
1 interface between chains.
- A–B · 650 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5T2T · Crystal structure of Lymphocytic choriomeningitis mammarenavirus endonuclease bound to… · 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 A0A059U382
- Elsewhere: RCSB PDB 5T2T · PDBe 5T2T · UniProt A0A059U382
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