Research workbench
Structure of S. pombe PCT1 RNA triphosphatase in complex with the SPT5 ctd
Analyse Structure of S. pombe PCT1 RNA triphosphatase in complex with the SPT5 ctd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PN1
- Type
- protein
- Length
- 1,055 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA-capping enzyme subunit beta; Synthetic peptide
- EC
- 3.1.3.33
- UniProt
- Q9P6Q6
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 25% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MRNA-capping enzyme subunit beta (EC 3.1.3.33) | protein | 259 | 25% helix, 38% strand | Q9P6Q6 |
| B | MRNA-capping enzyme subunit beta (EC 3.1.3.33) | protein | 261 | 25% helix, 39% strand | Q9P6Q6 |
| C | MRNA-capping enzyme subunit beta (EC 3.1.3.33) | protein | 256 | 25% helix, 39% strand | Q9P6Q6 |
| D | MRNA-capping enzyme subunit beta (EC 3.1.3.33) | protein | 255 | 25% helix, 38% strand | Q9P6Q6 |
| E, F, G, H | Synthetic peptide | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- FMT · Formic acid · additive · 6 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 789 | 0.74 | 0.79 | 75 | FMT |
| 2 | 450 | 0.68 | 0.80 | 48 | FMT |
| 3 | 430 | 0.60 | 0.75 | 57 | empty |
| 4 | 312 | 0.60 | 0.78 | 33 | empty |
| 5 | 388 | 0.59 | 0.76 | 53 | empty |
Interfaces
13 interfaces between chains.
- A–B · 2169 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2131 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 564 Ų buried · 12 hydrogen bonds · protein-protein
- D–H · 339 Ų buried · 2 hydrogen bonds · protein-protein
- B–F · 334 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4PN1 · Structure of S. pombe Pct1 RNA triphosphatase in complex with the Spt5 CTD · the same entry in another collection · chain H against H, TM-score 1.00
- Q9P6Q6 · AlphaFold monomer V2.0 prediction for mRNA-capping enzyme subunit beta (Q9P6Q6) · 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 Q9P6Q6
- Elsewhere: RCSB PDB 4PN1 · PDBe 4PN1 · UniProt Q9P6Q6
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