Research workbench
Cf IM25-cf IM68-uguaa complex
Analyse Cf IM25-cf IM68-uguaa complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P6Y
- Type
- protein + RNA
- Length
- 2,217 residues
- Chains
- 23
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cleavage and polyadenylation specificity factor subunit 5; Cleavage and polyadenylation…
- UniProt
- O43809, Q16630
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 13 distinct chains · 25% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | Cleavage and polyadenylation specificity factor subunit 5 | protein | 195 | 25% helix, 37% strand | O43809 |
| B, F, J, N | Cleavage and polyadenylation specificity factor subunit 5 | protein | 197 | 23% helix, 38% strand | O43809 |
| C | Cleavage and polyadenylation specificity factor subunit 6 | protein | 79 | 24% helix, 32% strand | Q16630 |
| D | Cleavage and polyadenylation specificity factor subunit 6 | protein | 78 | 31% helix, 31% strand | Q16630 |
| G, L | Cleavage and polyadenylation specificity factor subunit 6 | protein | 80 | 25% helix, 35% strand | Q16630 |
| H | Cleavage and polyadenylation specificity factor subunit 6 | protein | 74 | 27% helix, 30% strand | Q16630 |
| K, O | Cleavage and polyadenylation specificity factor subunit 6 | protein | 80 | 25% helix, 31% strand | Q16630 |
| M | Cleavage and polyadenylation specificity factor subunit 5 | protein | 196 | 23% helix, 37% strand | O43809 |
| P | Cleavage and polyadenylation specificity factor subunit 6 | protein | 75 | 29% helix, 31% strand | Q16630 |
| Q, W | 5'-R(*UP*GP*UP*AP*A)-3' | rna | 1 | — | — |
| R, S | 5'-R(*UP*GP*UP*AP*A)-3' | rna | 5 | — | — |
| T | 5'-R(*UP*GP*UP*AP*A)-3' | rna | 4 | — | — |
| U, V | 5'-R(*UP*GP*UP*AP*A)-3' | rna | 3 | — | — |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.79 | 0.81 | 112 | empty |
| 2 | 699 | 0.78 | 0.83 | 76 | empty |
| 3 | 737 | 0.77 | 0.82 | 77 | empty |
| 4 | 723 | 0.77 | 0.82 | 61 | empty |
| 5 | 502 | 0.75 | 0.83 | 44 | empty |
Interfaces
36 interfaces between chains.
- A–B · 1044 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 1040 Ų buried · 4 hydrogen bonds · protein-protein
- M–N · 1020 Ų buried · 5 hydrogen bonds · protein-protein
- I–J · 1005 Ų buried · 5 hydrogen bonds · protein-protein
- E–S · 551 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 3P6Y · CF Im25-CF Im68-UGUAA complex · the same entry in another collection · chain I against I, TM-score 1.00
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 O43809
- Every structure of UniProt Q16630
- Elsewhere: RCSB PDB 3P6Y · PDBe 3P6Y · UniProt O43809 · UniProt Q16630
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