Research workbench
Crystal structure of C. crescentus pnpase bound to RNA
Analyse Crystal structure of C. crescentus pnpase bound to RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AM3
- Type
- protein + RNA
- Length
- 1,873 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyribonucleotide nucleotidyltransferase; RNA, 5'-R(*UP*AP*AP*CP*UP*UP*UP*GP*GP)-3'
- EC
- 2.7.7.8
- UniProt
- Q9AC32
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8) | protein | 622 | 36% helix, 27% strand | Q9AC32 |
| B, C | Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8) | protein | 621 | 35% helix, 27% strand | Q9AC32 |
| E | RNA, 5'-R(*UP*AP*AP*CP*UP*UP*UP*GP*GP)-3' | rna | 9 | — | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 659 | 0.84 | 0.88 | 85 | empty |
| 2 | 635 | 0.83 | 0.88 | 86 | empty |
| 3 | 453 | 0.80 | 0.88 | 54 | empty |
| 4 | 818 | 0.68 | 0.75 | 76 | PO4 |
| 5 | 155 | 0.64 | 0.86 | 26 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2010 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1907 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1904 Ų buried · 32 hydrogen bonds · protein-protein
- A–E · 542 Ų buried · 5 hydrogen bonds · protein-nucleic
- C–E · 534 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 4AM3 · Crystal structure of C. crescentus PNPase bound to RNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q9AC32 · AlphaFold monomer V2.0 prediction for polyribonucleotide nucleotidyltransferase (Q9AC32) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9AC32
- Elsewhere: RCSB PDB 4AM3 · PDBe 4AM3 · UniProt Q9AC32
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