MolNFT v1 · #60885 · protein
2.2 a crystal structure of inorganic pyrophosphatase from rickettsia prowazekii
3D53: “2.2 a crystal structure of inorganic pyrophosphatase from rickettsia prowazekii”. X-ray diffraction, 1 ligand (CL), 14 pockets (best druggability 0.79). MolNFT v1 #60885 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3D53
- Type
- protein
- Length
- 1,016 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inorganic pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- Q9ZCW5
- Ligands
- CL
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 170 | 21% helix, 34% strand | Q9ZCW5 |
| C, D | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 171 | 21% helix, 34% strand | Q9ZCW5 |
| E, F | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 167 | 19% helix, 36% strand | Q9ZCW5 |
Ligands and binding sites
- CL · Chloride ion · ion · 20 copies · chains A, B, C, F, D, E
- GOL · Glycerol · additive · 3 copies · chains B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.79 | 0.81 | 92 | empty |
| 2 | 877 | 0.78 | 0.81 | 96 | empty |
| 3 | 495 | 0.77 | 0.85 | 58 | empty |
| 4 | 497 | 0.77 | 0.85 | 62 | empty |
| 5 | 461 | 0.75 | 0.84 | 59 | empty |
Interfaces
12 interfaces between chains.
- A–E · 727 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 723 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 720 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 713 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 708 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3D53 · 2.2 A crystal structure of inorganic pyrophosphatase from Rickettsia prowazekii · the same entry in another collection · chain F against F, TM-score 1.00
- Q9ZCW5 · AlphaFold monomer V2.0 prediction for inorganic pyrophosphatase (Q9ZCW5) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 3D53 · PDBe 3D53 · UniProt Q9ZCW5
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