Research workbench
Structure of the family II inorganic pyrophosphatase from streptococcus agalactiae at 2.8 resolution
Analyse Structure of the family II inorganic pyrophosphatase from streptococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ENX
- Type
- protein
- Length
- 620 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
- Q3K0B5
- Ligands
- 2PN, TRP, MN, MG
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Manganese-dependent inorganic pyrophosphatase (EC 3.6.1.1) | protein | 310 | 40% helix, 20% strand | Q3K0B5 |
Ligands and binding sites
- 2PN · Imidodiphosphoric acid · ligand · 2 copies · chains A, B
- TRP · Tryptophan · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.79 | 0.91 | 50 | MG, 2PN |
| 2 | 227 | 0.77 | 0.92 | 45 | MG, 2PN |
| 3 | 376 | 0.59 | 0.76 | 33 | empty |
| 4 | 78 | 0.48 | 0.82 | 13 | TRP |
| 5 | 54 | 0.44 | 0.83 | 13 | TRP |
Interfaces
1 interface between chains.
- A–B · 171 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2ENX · Structure of the family II inorganic pyrophosphatase from Streptococcus agalactiae at 2.8… · the same entry in another collection · chain B against B, TM-score 1.00
- Q3K0B5 · AlphaFold monomer V2.0 prediction for probable manganese-dependent inorganic… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q3K0B5
- Elsewhere: RCSB PDB 2ENX · PDBe 2ENX · UniProt Q3K0B5
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