Research workbench
Polymerase module of yeast cpf in complex with the ypim of CFT2
Analyse Polymerase module of yeast cpf in complex with the ypim of CFT2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZGQ
- Type
- protein
- Length
- 1,749 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cleavage factor two protein 2; Protein CFT1; MRNA 3'-end-processing protein YTH1…
- UniProt
- Q12102, Q06632, A0A6A5Q2R8, A0A6A5Q543
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 7% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Cleavage factor two protein 2 | protein | 38 | 0% helix, 16% strand | Q12102 |
| A | Protein CFT1 | protein | 1237 | 6% helix, 45% strand | Q06632 |
| B | MRNA 3'-end-processing protein YTH1 | protein | 90 | 19% helix, 4% strand | A0A6A5Q2R8 |
| D | Polyadenylation factor subunit 2 | protein | 384 | 7% helix, 38% strand | A0A6A5Q543 |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 685 | 0.84 | 0.88 | 70 | empty |
| 2 | 473 | 0.83 | 0.90 | 63 | empty |
| 3 | 125 | 0.81 | 0.99 | 25 | empty |
| 4 | 658 | 0.81 | 0.85 | 70 | empty |
| 5 | 502 | 0.79 | 0.86 | 61 | empty |
Interfaces
5 interfaces between chains.
- A–D · 3861 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 1923 Ų buried · 22 hydrogen bonds · protein-protein
- C–A · 926 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 736 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 308 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7ZGQ · Polymerase module of yeast CPF in complex with the yPIM of Cft2 · the same entry in another collection · chain C against C, 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 Q12102
- Every structure of UniProt Q06632
- Every structure of UniProt A0A6A5Q2R8
- Every structure of UniProt A0A6A5Q543
- Elsewhere: RCSB PDB 7ZGQ · PDBe 7ZGQ · UniProt Q12102 · UniProt Q06632 · UniProt A0A6A5Q2R8 · UniProt A0A6A5Q543
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