MolNFT v1 · #15387 · protein + RNA
Reovirus polymerase LAMBDA3 elongation complex with one phosphodiester bond formed
1N38 · 5'-R(P*GP*C)-3': “Reovirus polymerase LAMBDA3 elongation complex with one phosphodiester bond formed”. X-ray diffraction, 3 ligands (CH1, U3H, MN), 13 pockets (best druggability 0.81). MolNFT v1 #15387 on GenesisL1: 3D structure…
- PDB
- 1N38
- Type
- protein + RNA
- Length
- 1,271 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(P*GP*C)-3'; 5'-R(*AP*UP*UP*AP*GP*C)-3'; Minor core protein lambda 3
- UniProt
- P17378
- Ligands
- CH1, U3H, MN
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-R(P*GP*C)-3' | rna | 2 | — | — |
| C | 5'-R(*AP*UP*UP*AP*GP*C)-3' | rna | 5 | — | — |
| A | Minor core protein lambda 3 | protein | 1264 | 49% helix, 13% strand | P17378 |
Ligands and binding sites
- CH1 · 3'-deoxy-cytidine-5'-triphosphate · ligand · 2 copies · chains A
- U3H · 3'-deoxy-uridine 5'-triphosphate · ligand · chains B, C, A
- MN · Manganese (II) ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 782 | 0.81 | 0.84 | 84 | MN, U3H |
| 2 | 115 | 0.73 | 0.93 | 32 | empty |
| 3 | 582 | 0.73 | 0.80 | 66 | empty |
| 4 | 54 | 0.71 | 0.98 | 24 | empty |
| 5 | 605 | 0.70 | 0.79 | 78 | CH1 |
Interfaces
3 interfaces between chains.
- C–A · 749 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–A · 358 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–C · 97 Ų buried · 9 hydrogen bonds · nucleic-nucleic
Compared structures
- 1N38 · reovirus polymerase lambda3 elongation complex with one phosphodiester bond formed · the same entry in another collection · chain C against C, 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 P17378
- Elsewhere: RCSB PDB 1N38 · PDBe 1N38 · UniProt P17378
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.