MolNFT v1 · #88553 · protein
Chaetomium thermophilum PAN3
4CYI · Pab-dependent POLY(A)-specific ribonuclease subunit PAN3…: “Chaetomium thermophilum PAN3”. X-ray diffraction, 2 ligands (ATP, MG), 20 pockets (best druggability 0.76). MolNFT v1 #88553 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4CYI
- Type
- protein
- Length
- 3,221 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pab-dependent POLY(A)-specific ribonuclease subunit PAN3- like protein, pab-dependent…
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 8 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pab-dependent POLY(A)-specific ribonuclease subunit PAN3- like protein, pab-dependent POLY(A)-specific ribonuclease subunit PAN3-L protein | protein | 405 | 47% helix, 16% strand | — |
| B | Pab-dependent POLY(A)-specific ribonuclease subunit PAN3- like protein, pab-dependent POLY(A)-specific ribonuclease subunit PAN3-L protein | protein | 406 | 49% helix, 15% strand | — |
| C | Pab-dependent POLY(A)-specific ribonuclease subunit PAN3- like protein, pab-dependent POLY(A)-specific ribonuclease subunit PAN3-L protein | protein | 397 | 48% helix, 15% strand | — |
| D | Pab-dependent POLY(A)-specific ribonuclease subunit PAN3- like protein, pab-dependent POLY(A)-specific ribonuclease subunit PAN3-L protein | protein | 407 | 49% helix, 14% strand | — |
| E | Pab-dependent POLY(A)-specific ribonuclease subunit PAN3- like protein, pab-dependent POLY(A)-specific ribonuclease subunit PAN3-L protein | protein | 394 | 49% helix, 15% strand | — |
| F | Pab-dependent POLY(A)-specific ribonuclease subunit PAN3- like protein, pab-dependent POLY(A)-specific ribonuclease subunit PAN3-L protein | protein | 408 | 49% helix, 15% strand | — |
| G | Pab-dependent POLY(A)-specific ribonuclease subunit PAN3- like protein, pab-dependent POLY(A)-specific ribonuclease subunit PAN3-L protein | protein | 397 | 49% helix, 15% strand | — |
| H | Pab-dependent POLY(A)-specific ribonuclease subunit PAN3- like protein, pab-dependent POLY(A)-specific ribonuclease subunit PAN3-L protein | protein | 407 | 49% helix, 15% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 999 | 0.76 | 0.78 | 87 | ATP, MG |
| 2 | 897 | 0.76 | 0.79 | 75 | empty |
| 3 | 769 | 0.75 | 0.80 | 72 | ATP, MG |
| 4 | 801 | 0.75 | 0.79 | 62 | empty |
| 5 | 802 | 0.75 | 0.79 | 58 | empty |
Interfaces
11 interfaces between chains.
- C–D · 3650 Ų buried · 45 hydrogen bonds · protein-protein
- G–H · 3612 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 3599 Ų buried · 45 hydrogen bonds · protein-protein
- E–F · 3566 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 584 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 modified (engineered).
Compared structures
- 4CYI · Chaetomium thermophilum Pan3 · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 4CYI · PDBe 4CYI
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