MolNFT v1 · #32871 · protein
RNase pH core of the archaeal exosome in complex with A5 RNA
2C38 · Probable exosome complex exonuclease 2: “RNase pH core of the archaeal exosome in complex with A5 RNA”. X-ray diffraction, 2 ligands (AMP, CL), 20 pockets (best druggability 0.79). MolNFT v1 #32871 on GenesisL1: 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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