MolNFT v1 · #32870 · protein
RNase pH core of the archaeal exosome in complex with U8 RNA
2C37 · Probable exosome complex exonuclease 2: “RNase pH core of the archaeal exosome in complex with U8 RNA”. X-ray diffraction, 4 ligands (U5P, RP5, NA), 20 pockets (best druggability 0.74). MolNFT v1 #32870 on GenesisL1: 3D structure…
- PDB
- 2C37
- Type
- protein
- Length
- 6,044 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
- U5P, RP5, NA, CL
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 29% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q, S, U, W | Probable exosome complex exonuclease 2 (EC 3.1.13.-) | protein | 260 | 30% helix, 37% 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, T | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 247 | 28% helix, 33% strand | Q9UXC2 |
| P | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 248 | 28% helix, 33% strand | Q9UXC2 |
| R | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 245 | 29% helix, 33% strand | Q9UXC2 |
| V | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 244 | 29% helix, 34% strand | Q9UXC2 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · 25 copies · chains A, B, E, F, G, H, I, J, M, N, U, V, W, X
- RP5 · 5-O-phosphono-beta-D-ribofuranose · ligand · chains N
- NA · Sodium ion · metal · chains U, V
- 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 | 910 | 0.74 | 0.77 | 69 | empty |
| 2 | 863 | 0.74 | 0.78 | 68 | empty |
| 3 | 861 | 0.73 | 0.78 | 66 | empty |
| 4 | 941 | 0.73 | 0.77 | 65 | empty |
| 5 | 969 | 0.73 | 0.76 | 65 | empty |
Interfaces
48 interfaces between chains.
- Q–R · 1870 Ų buried · 35 hydrogen bonds · protein-protein
- U–V · 1866 Ų buried · 34 hydrogen bonds · protein-protein
- I–J · 1864 Ų buried · 38 hydrogen bonds · protein-protein
- M–N · 1864 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1861 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 2C37 · RNase pH core of the archaeal exosome in complex with U8 RNA · 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 2C37 · PDBe 2C37 · UniProt Q9UXC0 · UniProt Q9UXC2
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