MolNFT v1 · #134750 · protein
Crystal structure of an inorganic pyrophosphatase from neisseria gonorrhoeae
5TEA: “Crystal structure of an inorganic pyrophosphatase from neisseria gonorrhoeae”. X-ray diffraction, 2 ligands (CA, CL), 12 pockets (best druggability 0.80). MolNFT v1 #134750 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5TEA
- Type
- protein
- Length
- 1,042 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inorganic pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- Q9K0G4
- Ligands
- CA, CL
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 173 | 21% helix, 36% strand | Q9K0G4 |
| B, C, D, F | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 174 | 25% helix, 35% strand | Q9K0G4 |
| E | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 173 | 23% helix, 35% strand | Q9K0G4 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 7 copies · chains A, D, B, F, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.80 | 0.88 | 74 | empty |
| 2 | 356 | 0.78 | 0.88 | 60 | empty |
| 3 | 539 | 0.76 | 0.83 | 49 | CL |
| 4 | 570 | 0.75 | 0.82 | 56 | CL |
| 5 | 302 | 0.75 | 0.87 | 54 | empty |
Interfaces
12 interfaces between chains.
- B–C · 737 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 736 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 720 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 714 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 704 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5TEA · Crystal structure of an inorganic pyrophosphatase from Neisseria gonorrhoeae · the same entry in another collection · chain F against F, TM-score 1.00
- Q9K0G4 · AlphaFold monomer V2.0 prediction for inorganic pyrophosphatase (Q9K0G4) · a predicted model of the same protein · chain E 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 Q9K0G4
- Elsewhere: RCSB PDB 5TEA · PDBe 5TEA · UniProt Q9K0G4
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