MolNFT v1 · #140715 · protein
Crystal structure of pnpase from staphylococcus epidermidis
5YJJ · Polyribonucleotide nucleotidyltransferase: “Crystal structure of pnpase from staphylococcus epidermidis”. X-ray diffraction, 2 ligands (MG, PO4), 20 pockets (best druggability 0.65). MolNFT v1 #140715 on GenesisL1: 3D structure…
- PDB
- 5YJJ
- Type
- protein
- Length
- 2,651 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyribonucleotide nucleotidyltransferase
- EC
- 2.7.7.8
- UniProt
- Q8CST1
- Ligands
- MG, PO4
- Pockets
- 20 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F | Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8) | protein | 442 | 33% helix, 33% strand | Q8CST1 |
| E | Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8) | protein | 441 | 34% helix, 32% strand | Q8CST1 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.65 | 0.77 | 67 | PO4, MG |
| 2 | 588 | 0.64 | 0.75 | 67 | PO4, MG |
| 3 | 353 | 0.62 | 0.78 | 49 | empty |
| 4 | 315 | 0.59 | 0.78 | 40 | empty |
| 5 | 357 | 0.58 | 0.76 | 53 | empty |
Interfaces
11 interfaces between chains.
- B–C · 1353 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1322 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1321 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 1317 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1309 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5YJJ · Crystal structure of PNPase from Staphylococcus epidermidis · the same entry in another collection · chain F against F, TM-score 1.00
- Q8CST1 · AlphaFold monomer V2.0 prediction for polyribonucleotide nucleotidyltransferase (Q8CST1) · a predicted model of the same protein · chain A against A, TM-score 0.52
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 Q8CST1
- Elsewhere: RCSB PDB 5YJJ · PDBe 5YJJ · UniProt Q8CST1
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