Research workbench
RNase pH core of the archaeal exosome in complex with ADP
Analyse RNase pH core of the archaeal exosome in complex with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C39
- Type
- protein
- Length
- 6,022 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable exosome complex exonuclease 2; Probable exosome complex exonuclease 1
- EC
- 3.1.13.-
- UniProt
- Q9UXC0, Q9UXC2
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 11 distinct chains · 30% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q | Probable exosome complex exonuclease 2 (EC 3.1.13.-) | protein | 260 | 28% helix, 38% strand | Q9UXC0 |
| B, F, J | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 241 | 30% helix, 34% strand | Q9UXC2 |
| D, P, R, T | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 248 | 30% helix, 33% strand | Q9UXC2 |
| H | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 230 | 31% helix, 34% strand | Q9UXC2 |
| L | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 247 | 29% helix, 33% strand | Q9UXC2 |
| N | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 239 | 30% helix, 34% strand | Q9UXC2 |
| S | Probable exosome complex exonuclease 2 (EC 3.1.13.-) | protein | 259 | 29% helix, 37% strand | Q9UXC0 |
| U | Probable exosome complex exonuclease 2 (EC 3.1.13.-) | protein | 255 | 29% helix, 35% strand | Q9UXC0 |
| V | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 239 | 30% helix, 33% strand | Q9UXC2 |
| W | Probable exosome complex exonuclease 2 (EC 3.1.13.-) | protein | 259 | 29% helix, 37% strand | Q9UXC0 |
| X | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 239 | 30% helix, 32% strand | Q9UXC2 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 12 copies · chains B, D, F, H, J, L, N, P, R, T, V, X
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 | 970 | 0.74 | 0.77 | 73 | empty |
| 2 | 1020 | 0.73 | 0.76 | 79 | empty |
| 3 | 929 | 0.73 | 0.77 | 62 | empty |
| 4 | 901 | 0.72 | 0.77 | 70 | empty |
| 5 | 901 | 0.72 | 0.77 | 67 | empty |
Interfaces
48 interfaces between chains.
- Q–R · 1876 Ų buried · 32 hydrogen bonds · protein-protein
- M–N · 1863 Ų buried · 35 hydrogen bonds · protein-protein
- I–J · 1856 Ų buried · 35 hydrogen bonds · protein-protein
- U–V · 1856 Ų buried · 34 hydrogen bonds · protein-protein
- O–P · 1855 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 2C39 · RNase PH core of the archaeal exosome in complex with ADP · the same entry in another collection · chain K against K, 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 Q9UXC0
- Every structure of UniProt Q9UXC2
- Elsewhere: RCSB PDB 2C39 · PDBe 2C39 · UniProt Q9UXC0 · UniProt Q9UXC2
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