Research workbench
Crystal structure of S.AUREUS pnpase catalytic domain
Analyse Crystal structure of S.AUREUS pnpase catalytic domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XEX
- Type
- protein
- Length
- 3,071 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyribonucleotide nucleotidyltransferase
- EC
- 2.7.7.8
- UniProt
- Q2FZ20
- Ligands
- PPV
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 6 distinct chains · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8) | protein | 511 | 37% helix, 28% strand | Q2FZ20 |
| B | Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8) | protein | 510 | 37% helix, 28% strand | Q2FZ20 |
| C | Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8) | protein | 511 | 37% helix, 28% strand | Q2FZ20 |
| D | Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8) | protein | 515 | 36% helix, 28% strand | Q2FZ20 |
| E | Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8) | protein | 511 | 37% helix, 28% strand | Q2FZ20 |
| F | Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8) | protein | 513 | 37% helix, 28% strand | Q2FZ20 |
Ligands and binding sites
- PPV · Pyrophosphate · ligand · 6 copies · chains A, B, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1161 | 0.70 | 0.74 | 112 | PEG, PPV |
| 2 | 861 | 0.68 | 0.75 | 71 | PEG, PPV |
| 3 | 563 | 0.68 | 0.78 | 75 | empty |
| 4 | 566 | 0.67 | 0.78 | 81 | empty |
| 5 | 546 | 0.67 | 0.78 | 76 | empty |
Interfaces
8 interfaces between chains.
- E–F · 1303 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1301 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1297 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 1258 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1247 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5XEX · Crystal structure of S.aureus PNPase catalytic domain · the same entry in another collection · chain F against F, TM-score 1.00
- Q2FZ20 · AlphaFold monomer V2.0 prediction for polyribonucleotide nucleotidyltransferase (Q2FZ20) · a predicted model of the same protein · chain F 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 Q2FZ20
- Elsewhere: RCSB PDB 5XEX · PDBe 5XEX · UniProt Q2FZ20
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