MolNFT v1 · #35422 · protein
Crystal structure of methanococcus jannaschii putative family II inorganic pyrophosphatase
2EB0 · Manganese-dependent inorganic pyrophosphatase: “Crystal structure of methanococcus jannaschii putative family II inorganic pyrophosphatase”. X-ray diffraction, 1 ligand (MN), 5 pockets (best druggability 0.81). MolNFT v1 #35422 on…
- PDB
- 2EB0
- Type
- protein
- Length
- 611 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Manganese-dependent inorganic pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- Q58025
- Ligands
- MN
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Manganese-dependent inorganic pyrophosphatase (EC 3.6.1.1) | protein | 304 | 44% helix, 20% strand | Q58025 |
| B | Manganese-dependent inorganic pyrophosphatase (EC 3.6.1.1) | protein | 307 | 44% helix, 21% strand | Q58025 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.81 | 0.96 | 40 | empty |
| 2 | 264 | 0.78 | 0.91 | 48 | empty |
| 3 | 363 | 0.58 | 0.76 | 47 | empty |
| 4 | 150 | 0.44 | 0.75 | 27 | empty |
| 5 | 92 | 0.35 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1286 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 2EB0 · Crystal structure of Methanococcus jannaschii putative family II inorganic pyrophosphatase · the same entry in another collection · chain A against A, TM-score 1.00
- Q58025 · AlphaFold monomer V2.0 prediction for manganese-dependent inorganic pyrophosphatase… · a predicted model of the same protein · chain A against A, TM-score 0.66
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 Q58025
- Elsewhere: RCSB PDB 2EB0 · PDBe 2EB0 · UniProt Q58025
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