MolNFT v1 · #191032 · protein
Polymerase module of yeast cpf in complex with the ypim of CFT2
7ZGQ · Cleavage factor two protein 2: “Polymerase module of yeast cpf in complex with the ypim of CFT2”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #191032 on GenesisL1: 3D structure, binding sites and pockets in…
- 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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