Research workbench
Complex of neurospora crassa PAN2 (WD40-CS1) with PAN3 (pseudokinase and C-term)
Analyse Complex of neurospora crassa PAN2 (WD40-CS1) with PAN3 (pseudokinase and C-term) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CZY
- Type
- protein
- Length
- 1,452 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pab-dependent POLY(A)-specific ribonuclease subunit PAN2; Pab-dependent POLY(A)-specific…
- EC
- 3.1.13.4
- UniProt
- P0C581, Q7SDP4
- Ligands
- ANP, MG
- Pockets
- 18 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Pab-dependent POLY(A)-specific ribonuclease subunit PAN2 (EC 3.1.13.4) | protein | 323 | 2% helix, 48% strand | P0C581 |
| B | Pab-dependent POLY(A)-specific ribonuclease subunit PAN3 | protein | 403 | 47% helix, 15% strand | Q7SDP4 |
| D | Pab-dependent POLY(A)-specific ribonuclease subunit PAN3 | protein | 403 | 46% helix, 15% strand | Q7SDP4 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains B, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 753 | 0.75 | 0.80 | 62 | MES |
| 2 | 721 | 0.74 | 0.80 | 59 | MES |
| 3 | 733 | 0.73 | 0.79 | 62 | empty |
| 4 | 60 | 0.72 | 0.97 | 23 | empty |
| 5 | 341 | 0.70 | 0.83 | 41 | ANP, MG |
Interfaces
3 interfaces between chains.
- B–D · 3369 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 723 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 712 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4CZY · Complex of Neurospora crassa PAN2 (WD40-CS1) with PAN3 (pseudokinase and C-term) · the same entry in another collection · chain A against A, TM-score 1.00
- P0C581 · 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 0.95
- Q7SDP4 · AlphaFold monomer V2.0 prediction for PAN2-PAN3 deadenylation complex subunit PAN3… · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P0C581
- Every structure of UniProt Q7SDP4
- Elsewhere: RCSB PDB 4CZY · PDBe 4CZY · UniProt P0C581 · UniProt Q7SDP4
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