Research workbench
Polya polymerase module of the cleavage and polyadenylation factor (cpf) from saccharomyces cerevisiae
Analyse Polya polymerase module of the cleavage and polyadenylation factor (cpf) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EOJ
- Type
- protein
- Length
- 1,715 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein CFT1; MRNA 3'-end-processing protein YTH1; Polyadenylation factor subunit…
- UniProt
- Q06632, Q06102, P42841
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 6% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein CFT1 | protein | 1233 | 6% helix, 44% strand | Q06632 |
| B | MRNA 3'-end-processing protein YTH1 | protein | 94 | 12% helix, 4% strand | Q06102 |
| D | Polyadenylation factor subunit 2,POLYADENYLATION factor subunit 2 | protein | 388 | 6% helix, 37% strand | P42841 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1157 | 0.87 | 0.89 | 87 | empty |
| 2 | 1129 | 0.82 | 0.83 | 110 | empty |
| 3 | 86 | 0.77 | 0.99 | 21 | empty |
| 4 | 588 | 0.77 | 0.83 | 45 | empty |
| 5 | 826 | 0.76 | 0.80 | 68 | empty |
Interfaces
3 interfaces between chains.
- A–D · 4355 Ų buried · 58 hydrogen bonds · protein-protein
- A–B · 2119 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 397 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6EOJ · PolyA polymerase module of the cleavage and polyadenylation factor (CPF) from… · the same entry in another collection · chain D against D, TM-score 1.00
- Q06632 · AlphaFold monomer V2.0 prediction for protein CFT1 (Q06632) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P42841 · AlphaFold monomer V2.0 prediction for polyadenylation factor subunit 2 (P42841) · a predicted model of the same protein · chain D against A, TM-score 0.94
- Q06102 · AlphaFold monomer V2.0 prediction for mRNA 3'-end-processing protein YTH1 (Q06102) · a predicted model of the same protein · chain B against A, TM-score 0.62
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 Q06632
- Every structure of UniProt Q06102
- Every structure of UniProt P42841
- Elsewhere: RCSB PDB 6EOJ · PDBe 6EOJ · UniProt Q06632 · UniProt Q06102 · UniProt P42841
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