Research workbench
RNase pH core of the archaeal exosome in complex with A5 RNA
Analyse RNase pH core of the archaeal exosome in complex with A5 RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C38
- Type
- protein
- Length
- 6,172 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
- AMP, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 28% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q, S, W | Probable exosome complex exonuclease 2 (EC 3.1.13.-) | protein | 271 | 28% helix, 36% strand | Q9UXC0 |
| B, F, H, J, N, X | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 241 | 29% helix, 34% strand | Q9UXC2 |
| D, L, R, T | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 247 | 28% helix, 32% strand | Q9UXC2 |
| P | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 248 | 28% helix, 32% strand | Q9UXC2 |
| U | Probable exosome complex exonuclease 2 (EC 3.1.13.-) | protein | 270 | 28% helix, 36% strand | Q9UXC0 |
| V | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 239 | 29% helix, 34% strand | Q9UXC2 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 28 copies · chains A, B, E, F, G, H, I, J, M, N, U, V, W, X
- CL · Chloride ion · ion · 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 | 1175 | 0.79 | 0.81 | 114 | empty |
| 2 | 1104 | 0.79 | 0.81 | 105 | empty |
| 3 | 885 | 0.79 | 0.81 | 85 | empty |
| 4 | 863 | 0.79 | 0.81 | 74 | empty |
| 5 | 825 | 0.78 | 0.81 | 85 | empty |
Interfaces
60 interfaces between chains.
- U–V · 1884 Ų buried · 35 hydrogen bonds · protein-protein
- W–X · 1882 Ų buried · 36 hydrogen bonds · protein-protein
- K–L · 1859 Ų buried · 37 hydrogen bonds · protein-protein
- I–J · 1859 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 1854 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 2C38 · RNase PH core of the archaeal exosome in complex with A5 RNA · the same entry in another collection · chain J against J, 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 2C38 · PDBe 2C38 · UniProt Q9UXC0 · UniProt Q9UXC2
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