Research workbench
Polymerase module of yeast cpf in complex with MPE1, the ypim of CFT2 and the pre-cleaved CYC1 RNA
Analyse Polymerase module of yeast cpf in complex with MPE1, the ypim of CFT2 and the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZGR
- Type
- protein + RNA
- Length
- 1,822 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein CFT1; MRNA 3'-end-processing protein YTH1; Cleavage factor two protein 2…
- UniProt
- Q06632, A0A6A5Q2R8, Q12102, A0A6A5Q543, A0A6A5PV64
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 6 distinct chains · 9% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein CFT1 | protein | 1254 | 7% helix, 45% strand | Q06632 |
| B | MRNA 3'-end-processing protein YTH1 | protein | 94 | 24% helix, 6% strand | A0A6A5Q2R8 |
| C | Cleavage factor two protein 2 | protein | 30 | 10% helix, 10% strand | Q12102 |
| D | Polyadenylation factor subunit 2 | protein | 395 | 8% helix, 37% strand | A0A6A5Q543 |
| E | Pre-cleaved CYC1 | rna | 3 | — | — |
| F | MPE1 isoform 1 | protein | 46 | 24% helix, 24% strand | A0A6A5PV64 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.85 | 0.87 | 85 | empty |
| 2 | 809 | 0.85 | 0.88 | 87 | empty |
| 3 | 709 | 0.84 | 0.87 | 97 | empty |
| 4 | 191 | 0.83 | 0.97 | 31 | empty |
| 5 | 502 | 0.83 | 0.90 | 55 | empty |
Interfaces
10 interfaces between chains.
- A–D · 3865 Ų buried · 59 hydrogen bonds · protein-protein
- A–B · 1886 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 844 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 798 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 774 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7ZGR · Polymerase module of yeast CPF in complex with Mpe1, the yPIM of Cft2 and the pre-cleaved… · the same entry in another collection · chain F against F, 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 0.99
- Q12102 · AlphaFold monomer V2.0 prediction for cleavage factor two protein 2 (Q12102) · a predicted model of the same protein · chain C against A, TM-score 0.42
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 A0A6A5Q2R8
- Every structure of UniProt Q12102
- Every structure of UniProt A0A6A5Q543
- Every structure of UniProt A0A6A5PV64
- Elsewhere: RCSB PDB 7ZGR · PDBe 7ZGR · UniProt Q06632 · UniProt A0A6A5Q2R8 · UniProt Q12102 · UniProt A0A6A5Q543 · UniProt A0A6A5PV64
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