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2.2 a crystal structure of inorganic pyrophosphatase from rickettsia prowazekii (P21 form)
Analyse 2.2 a crystal structure of inorganic pyrophosphatase from rickettsia prowazekii… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EMJ
- Type
- protein
- Length
- 1,978 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inorganic pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- Q9ZCW5
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 20% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, J | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 167 | 19% helix, 35% strand | Q9ZCW5 |
| B, G | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 166 | 19% helix, 40% strand | Q9ZCW5 |
| C, K | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 168 | 20% helix, 37% strand | Q9ZCW5 |
| D, H | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 170 | 19% helix, 36% strand | Q9ZCW5 |
| E, L | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 158 | 20% helix, 38% strand | Q9ZCW5 |
| F, I | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 160 | 20% helix, 36% strand | Q9ZCW5 |
Ligands and binding sites
- PG4 · Tetraethylene glycol · additive · 2 copies · chains E, L
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 | 972 | 0.83 | 0.84 | 123 | empty |
| 2 | 532 | 0.77 | 0.84 | 62 | empty |
| 3 | 619 | 0.77 | 0.83 | 62 | empty |
| 4 | 483 | 0.76 | 0.84 | 64 | empty |
| 5 | 464 | 0.75 | 0.84 | 63 | empty |
Interfaces
29 interfaces between chains.
- C–F · 740 Ų buried · 10 hydrogen bonds · protein-protein
- G–J · 740 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 732 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 730 Ų buried · 11 hydrogen bonds · protein-protein
- H–I · 720 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3EMJ · 2.2 A crystal structure of inorganic pyrophosphatase from rickettsia prowazekii (p21 form) · the same entry in another collection · chain L against L, 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 Q9ZCW5
- Elsewhere: RCSB PDB 3EMJ · PDBe 3EMJ · UniProt Q9ZCW5
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