MolNFT v1 · #103652 · protein
Structure of S. pombe PCT1 RNA triphosphatase in complex with the SPT5 ctd
4PN1 · MRNA-capping enzyme subunit beta: “Structure of S. pombe PCT1 RNA triphosphatase in complex with the SPT5 ctd”. X-ray diffraction, 13 pockets (best druggability 0.74). MolNFT v1 #103652 on GenesisL1: 3D structure, binding sites and…
- 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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