MolNFT v1 · #15330 · protein + RNA
Initiation complex of polymerase LAMBDA3 from reovirus
1N1H · 5'-R(*AP*UP*UP*AP*GP*C)-3': “Initiation complex of polymerase LAMBDA3 from reovirus”. X-ray diffraction, 5 ligands (G7M, GDP, CH1), 15 pockets (best druggability 0.79). MolNFT v1 #15330 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1N1H
- Type
- protein + RNA
- Length
- 1,268 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*AP*UP*UP*AP*GP*C)-3'; Minor core protein lambda 3
- UniProt
- P17378
- Ligands
- G7M, GDP, CH1, GH3, MN
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-R(*AP*UP*UP*AP*GP*C)-3' | rna | 4 | — | — |
| A | Minor core protein lambda 3 | protein | 1264 | 48% helix, 13% strand | P17378 |
Ligands and binding sites
- G7M · N7-methyl-guanosine-5'-monophosphate · ligand · chains A
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- CH1 · 3'-deoxy-cytidine-5'-triphosphate · ligand · chains B, A
- GH3 · 3'-deoxy-guanosine-5'-triphosphate · ligand · chains B, 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
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.79 | 0.96 | 38 | empty |
| 2 | 764 | 0.77 | 0.81 | 79 | MN, CH1, GH3 |
| 3 | 62 | 0.72 | 0.98 | 25 | empty |
| 4 | 835 | 0.71 | 0.77 | 83 | G7M |
| 5 | 845 | 0.70 | 0.76 | 77 | empty |
Interfaces
1 interface between chains.
- B–A · 663 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 1N1H · Initiation complex of polymerase lambda3 from reovirus · 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 P17378
- Elsewhere: RCSB PDB 1N1H · PDBe 1N1H · UniProt P17378
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