MolNFT v1 · #147813 · protein
Polya polymerase module of the cleavage and polyadenylation factor (cpf) from saccharomyces cerevisiae
6EOJ · Protein CFT1: “Polya polymerase module of the cleavage and polyadenylation factor (cpf) from saccharomyces cerevisiae”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.87). MolNFT v1 #147813 on GenesisL1: 3D…
- 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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