MolNFT v1 · #62415 · protein
Structure of the RNA pyrophosphohydrolase bdrpph in complex with holmium
3EEU · Probable pyrophosphohydrolase: “Structure of the RNA pyrophosphohydrolase bdrpph in complex with holmium”. X-ray diffraction, 2 ligands (HO, CL), 4 pockets (best druggability 0.60). MolNFT v1 #62415 on GenesisL1: 3D structure…
- PDB
- 3EEU
- Type
- protein
- Length
- 262 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable pyrophosphohydrolase
- EC
- 3.6.1.-
- UniProt
- Q6MPX4
- Ligands
- HO, CL
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable pyrophosphohydrolase (EC 3.6.1.-) | protein | 133 | 24% helix, 40% strand | Q6MPX4 |
| B | Probable pyrophosphohydrolase (EC 3.6.1.-) | protein | 129 | 22% helix, 40% strand | Q6MPX4 |
Ligands and binding sites
- HO · Holmium atom · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.60 | 0.82 | 25 | empty |
| 2 | 151 | 0.53 | 0.80 | 21 | CL |
| 3 | 92 | 0.35 | 0.74 | 14 | empty |
| 4 | 81 | 0.32 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1000 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3EEU · Structure of the RNA pyrophosphohydrolase BdRppH in complex with Holmium · 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
- Every structure of UniProt Q6MPX4
- Elsewhere: RCSB PDB 3EEU · PDBe 3EEU · UniProt Q6MPX4
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