Research workbench
Cryo-EM structure of a POLY(A) rnp bound to the PAN2-PAN3 deadenylase
Analyse Cryo-EM structure of a POLY(A) rnp bound to the PAN2-PAN3 deadenylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R5K
- Type
- protein + RNA
- Length
- 2,932 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PAN2-PAN3 deadenylation complex catalytic subunit PAN2; Polyadenylate-binding protein…
- EC
- 3.1.13.4
- UniProt
- P53010, P04147, P36102
- Ligands
- MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 7 distinct chains · 28% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PAN2-PAN3 deadenylation complex catalytic subunit PAN2 (EC 3.1.13.4) | protein | 1040 | 19% helix, 23% strand | P53010 |
| D | Polyadenylate-binding protein, cytoplasmic and nuclear | protein | 390 | 29% helix, 15% strand | P04147 |
| E | POLY(A) RNA | rna | 67 | — | — |
| F | Polyadenylate-binding protein, cytoplasmic and nuclear | protein | 165 | 21% helix, 18% strand | P04147 |
| H | Polyadenylate-binding protein, cytoplasmic and nuclear | protein | 394 | 28% helix, 18% strand | P04147 |
| N | PAN2-PAN3 deadenylation complex subunit PAN3 | protein | 429 | 41% helix, 8% strand | P36102 |
| O | PAN2-PAN3 deadenylation complex subunit PAN3 | protein | 447 | 40% helix, 10% strand | P36102 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 756 | 0.84 | 0.87 | 97 | empty |
| 2 | 1053 | 0.84 | 0.85 | 112 | empty |
| 3 | 730 | 0.83 | 0.86 | 87 | empty |
| 4 | 754 | 0.82 | 0.86 | 79 | empty |
| 5 | 277 | 0.81 | 0.92 | 45 | empty |
Interfaces
15 interfaces between chains.
- E–H · 4499 Ų buried · 143 hydrogen bonds · protein-nucleic
- N–O · 3816 Ų buried · 33 hydrogen bonds · protein-protein
- D–E · 3351 Ų buried · 83 hydrogen bonds · protein-nucleic
- A–N · 2928 Ų buried · 35 hydrogen bonds · protein-protein
- A–O · 2440 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 6R5K · Cryo-EM structure of a poly(A) RNP bound to the Pan2-Pan3 deadenylase · the same entry in another collection · chain O against O, TM-score 1.00
- P36102 · AlphaFold monomer V2.0 prediction for PAN2-PAN3 deadenylation complex subunit PAN3… · a predicted model of the same protein · chain O against A, TM-score 0.92
- P53010 · AlphaFold monomer V2.0 prediction for PAN2-PAN3 deadenylation complex catalytic subunit… · a predicted model of the same protein · chain A against A, TM-score 0.72
- P04147 · AlphaFold monomer V2.0 prediction for polyadenylate-binding protein, cytoplasmic and… · a predicted model of the same protein · chain F against A, TM-score 0.72
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 P53010
- Every structure of UniProt P04147
- Every structure of UniProt P36102
- Elsewhere: RCSB PDB 6R5K · PDBe 6R5K · UniProt P53010 · UniProt P04147 · UniProt P36102
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