MolNFT v1 · #80250 · protein
Structure of an inorganic pyrophosphatase (ppa) from coxiella burnetii
3TR4: “Structure of an inorganic pyrophosphatase (ppa) from coxiella burnetii”. X-ray diffraction, 2 ligands (MN, MG), 18 pockets (best druggability 0.80). MolNFT v1 #80250 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3TR4
- Type
- protein
- Length
- 1,017 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inorganic pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- Q83DR7
- Ligands
- MN, MG
- Pockets
- 18 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 21% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 169 | 21% helix, 37% strand | Q83DR7 |
| B, E | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 171 | 20% helix, 36% strand | Q83DR7 |
| C | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 168 | 21% helix, 37% strand | Q83DR7 |
| D | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 168 | 20% helix, 36% strand | Q83DR7 |
| F | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 170 | 22% helix, 36% strand | Q83DR7 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.80 | 0.82 | 95 | MN |
| 2 | 1032 | 0.78 | 0.80 | 71 | empty |
| 3 | 294 | 0.75 | 0.87 | 25 | empty |
| 4 | 1116 | 0.75 | 0.78 | 73 | empty |
| 5 | 260 | 0.75 | 0.88 | 25 | empty |
Interfaces
12 interfaces between chains.
- D–F · 752 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 720 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 706 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 705 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 685 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 3TR4 · Structure of an inorganic pyrophosphatase (ppa) from Coxiella burnetii · 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 Q83DR7
- Elsewhere: RCSB PDB 3TR4 · PDBe 3TR4 · UniProt Q83DR7
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