MolNFT v1 · #146635 · protein + RNA
Cryo-EM structure of human cpsf-160-WDR33-cpsf-30-pas RNA complex at 3.4 a resolution
6DNH · Cleavage and polyadenylation specificity factor subunit 1: “Cryo-EM structure of human cpsf-160-WDR33-cpsf-30-pas RNA complex at 3.4 a resolution”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.88). MolNFT v1…
- PDB
- 6DNH
- Type
- protein + RNA
- Length
- 1,677 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cleavage and polyadenylation specificity factor subunit 1; Pre-mRNA 3' end processing…
- UniProt
- Q10570, Q9C0J8, O95639
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 4 distinct chains · 6% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cleavage and polyadenylation specificity factor subunit 1 | protein | 1177 | 5% helix, 45% strand | Q10570 |
| B | Pre-mRNA 3' end processing protein WDR33 | protein | 376 | 5% helix, 34% strand | Q9C0J8 |
| C | Cleavage and polyadenylation specificity factor subunit 4 | protein | 117 | 16% helix, 5% strand | O95639 |
| E | RNA (5'-R(P*AP*AP*UP*AP*AP*AP*C)-3') | rna | 7 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains C
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 | 1146 | 0.88 | 0.89 | 101 | empty |
| 2 | 1153 | 0.86 | 0.87 | 108 | empty |
| 3 | 501 | 0.85 | 0.92 | 59 | empty |
| 4 | 709 | 0.85 | 0.89 | 83 | empty |
| 5 | 592 | 0.83 | 0.89 | 50 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3981 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 1917 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 907 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 700 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–E · 643 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 6DNH · Cryo-EM structure of human CPSF-160-WDR33-CPSF-30-PAS RNA complex at 3.4 A resolution · the same entry in another collection · chain A against A, TM-score 1.00
- Q9C0J8 · AlphaFold monomer V2.0 prediction for pre-mRNA 3' end processing protein WDR33 (Q9C0J8) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q10570 · AlphaFold monomer V2.0 prediction for cleavage and polyadenylation specificity factor… · a predicted model of the same protein · chain A against A, TM-score 0.99
- O95639 · AlphaFold monomer V2.0 prediction for cleavage and polyadenylation specificity factor… · a predicted model of the same protein · chain C against A, TM-score 0.93
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 Q10570
- Every structure of UniProt Q9C0J8
- Every structure of UniProt O95639
- Elsewhere: RCSB PDB 6DNH · PDBe 6DNH · UniProt Q10570 · UniProt Q9C0J8 · UniProt O95639
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