Research workbench
Polymerase module of cpf in complex with MPE1 and a pre-cleaved CYC1 RNA
Analyse Polymerase module of cpf in complex with MPE1 and a pre-cleaved CYC1 RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZGP
- Type
- protein + RNA
- Length
- 1,770 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein CFT1; MRNA 3'-end-processing protein YTH1; Polyadenylation factor subunit 2…
- UniProt
- Q06632, A0A6A5Q2R8, A0A6A5Q543, A0A6A5PV64
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 8% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein CFT1 | protein | 1236 | 7% helix, 46% strand | Q06632 |
| B | MRNA 3'-end-processing protein YTH1 | protein | 93 | 22% helix, 6% strand | A0A6A5Q2R8 |
| D | Polyadenylation factor subunit 2 | protein | 392 | 9% helix, 39% strand | A0A6A5Q543 |
| E | Pre-cleaved CYC1 | rna | 3 | — | — |
| F | MPE1 isoform 1 | protein | 46 | 20% 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.83 | 0.84 | 67 | empty |
| 2 | 496 | 0.83 | 0.90 | 54 | empty |
| 3 | 786 | 0.82 | 0.85 | 83 | empty |
| 4 | 152 | 0.82 | 0.98 | 26 | empty |
| 5 | 938 | 0.81 | 0.83 | 75 | empty |
Interfaces
8 interfaces between chains.
- A–D · 3832 Ų buried · 60 hydrogen bonds · protein-protein
- A–B · 1840 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 825 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 439 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–F · 389 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
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 A0A6A5Q543
- Every structure of UniProt A0A6A5PV64
- Elsewhere: RCSB PDB 7ZGP · PDBe 7ZGP · UniProt Q06632 · UniProt A0A6A5Q2R8 · UniProt A0A6A5Q543 · UniProt A0A6A5PV64
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