MolNFT v1 · #104052 · protein
PCE1 guanylyltransferase bound to SER2/SER5 phosphorylated RNA pol II ctd
4PZ6 · MRNA-capping enzyme subunit alpha: “PCE1 guanylyltransferase bound to SER2/SER5 phosphorylated RNA pol II ctd”. X-ray diffraction, 1 ligand (GMP), 12 pockets (best druggability 0.81). MolNFT v1 #104052 on GenesisL1: 3D structure…
- PDB
- 4PZ6
- Type
- protein
- Length
- 761 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA-capping enzyme subunit alpha; DNA-directed RNA polymerase II subunit RPB1
- EC
- 2.7.7.50
- UniProt
- P40997, P36594
- Ligands
- GMP
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MRNA-capping enzyme subunit alpha (EC 2.7.7.50) | protein | 373 | 27% helix, 32% strand | P40997 |
| B | MRNA-capping enzyme subunit alpha (EC 2.7.7.50) | protein | 372 | 27% helix, 33% strand | P40997 |
| P, Q | DNA-directed RNA polymerase II subunit RPB1 | protein | 8 | 0% helix, 0% strand | P36594 |
Ligands and binding sites
- GMP · Guanosine · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 763 | 0.81 | 0.84 | 83 | empty |
| 2 | 147 | 0.66 | 0.87 | 31 | GMP |
| 3 | 293 | 0.65 | 0.81 | 47 | empty |
| 4 | 235 | 0.55 | 0.78 | 31 | empty |
| 5 | 118 | 0.45 | 0.77 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1063 Ų buried · 15 hydrogen bonds · protein-protein
- B–P · 618 Ų buried · 10 hydrogen bonds · protein-protein
- A–Q · 576 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (phosphorylation).
Compared structures
- 4PZ6 · PCE1 guanylyltransferase bound to SER2/SER5 phosphorylated RNA pol II CTD · the same entry in another collection · chain A against A, TM-score 1.00
- P40997 · AlphaFold monomer V2.0 prediction for mRNA-capping enzyme subunit alpha (P40997) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P36594 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase II subunit RPB1 (P36594) · a predicted model of the same protein · chain P against A, TM-score 0.56
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 P40997
- Every structure of UniProt P36594
- Elsewhere: RCSB PDB 4PZ6 · PDBe 4PZ6 · UniProt P40997 · UniProt P36594
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