Research workbench
Crystal structure of polynucleotide phosphorylase in complex with RNase E and manganese
Analyse Crystal structure of polynucleotide phosphorylase in complex with RNase E and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GME
- Type
- protein
- Length
- 503 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyribonucleotide nucleotidyltransferase; Ribonuclease E
- EC
- 2.7.7.8, 3.1.4.-
- UniProt
- A7ZS61, A7ZKI9
- Ligands
- MN
- Pockets
- 1 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8) | protein | 482 | 30% helix, 30% strand | A7ZS61 |
| D | Ribonuclease E (EC 3.1.4.-) | protein | 21 | 0% helix, 24% strand | A7ZKI9 |
Ligands and binding sites
- 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
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 819 | 0.71 | 0.77 | 104 | MN |
Interfaces
1 interface between chains.
- A–D · 871 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3GME · Crystal Structure of Polynucleotide Phosphorylase in complex with RNase E and manganese · the same entry in another collection · chain D against D, TM-score 1.00
- A7ZS61 · AlphaFold monomer V2.0 prediction for polyribonucleotide nucleotidyltransferase (A7ZS61) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 A7ZS61
- Every structure of UniProt A7ZKI9
- Elsewhere: RCSB PDB 3GME · PDBe 3GME · UniProt A7ZS61 · UniProt A7ZKI9
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