MolNFT v1 · #54219 · protein
N-terminal endonuclease domain of la crosse virus L-protein
2XI7 · RNA polymerase L: “N-terminal endonuclease domain of la crosse virus L-protein”. X-ray diffraction, 2 ligands (XI7, MN), 2 pockets (best druggability 0.75). MolNFT v1 #54219 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2XI7
- Type
- protein
- Length
- 733 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA polymerase L
- UniProt
- A5HC98
- Ligands
- XI7, MN
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA polymerase L | protein | 184 | 50% helix, 14% strand | A5HC98 |
| B, C, D | RNA polymerase L | protein | 183 | 51% helix, 14% strand | A5HC98 |
Ligands and binding sites
- XI7 · 2-4-dioxo-4-phenylbutanoic acid · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 815 | 0.75 | 0.80 | 81 | MN, XI7 |
| 2 | 83 | 0.32 | 0.74 | 17 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1249 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 427 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 426 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 297 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2XI7 · N-terminal endonuclease domain of La Crosse virus L-protein · 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 A5HC98
- Elsewhere: RCSB PDB 2XI7 · PDBe 2XI7 · UniProt A5HC98
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