MolNFT v1 · #100917 · protein
Structure of the polynucleotide phosphorylase (CBU_0852) from coxiella burnetii
4NBQ · Polyribonucleotide nucleotidyltransferase: “Structure of the polynucleotide phosphorylase (CBU_0852) from coxiella burnetii”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.85). MolNFT v1 #100917 on GenesisL1: 3D…
- PDB
- 4NBQ
- Type
- protein
- Length
- 1,934 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyribonucleotide nucleotidyltransferase
- EC
- 2.7.7.8
- UniProt
- Q83D87
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.85
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 | 659 | 34% helix, 26% strand | Q83D87 |
| B | Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8) | protein | 668 | 34% helix, 28% strand | Q83D87 |
| C | Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8) | protein | 607 | 36% helix, 28% strand | Q83D87 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 13 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.85 | 0.86 | 124 | SO4 |
| 2 | 771 | 0.82 | 0.85 | 93 | empty |
| 3 | 543 | 0.80 | 0.86 | 62 | empty |
| 4 | 811 | 0.71 | 0.77 | 83 | SO4 |
| 5 | 204 | 0.69 | 0.87 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2516 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2178 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1952 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 47 modified (engineered).
Compared structures
- 4NBQ · Structure of the polynucleotide phosphorylase (CBU_0852) from Coxiella burnetii · the same entry in another collection · chain A against A, TM-score 1.00
- Q83D87 · AlphaFold monomer V2.0 prediction for polyribonucleotide nucleotidyltransferase (Q83D87) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 Q83D87
- Elsewhere: RCSB PDB 4NBQ · PDBe 4NBQ · UniProt Q83D87
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