Research workbench
The crystal structure of phosphopantetheinyl hydrolase (ppth) from mycobacterium tuberculosis
Analyse The crystal structure of phosphopantetheinyl hydrolase (ppth) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UNC
- Type
- protein
- Length
- 1,118 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallophos domain-containing protein
- UniProt
- I6YEE1
- Ligands
- MN, FE
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallophos domain-containing protein | protein | 278 | 31% helix, 18% strand | I6YEE1 |
| B | Metallophos domain-containing protein | protein | 282 | 30% helix, 18% strand | I6YEE1 |
| C | Metallophos domain-containing protein | protein | 281 | 30% helix, 18% strand | I6YEE1 |
| D | Metallophos domain-containing protein | protein | 277 | 31% helix, 18% strand | I6YEE1 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 893 | 0.73 | 0.77 | 84 | empty |
| 2 | 210 | 0.59 | 0.81 | 41 | empty |
| 3 | 258 | 0.56 | 0.78 | 42 | empty |
| 4 | 62 | 0.51 | 0.86 | 19 | empty |
| 5 | 232 | 0.50 | 0.75 | 37 | empty |
Interfaces
5 interfaces between chains.
- B–C · 624 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 604 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 259 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 203 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 156 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 6UNC · The crystal structure of Phosphopantetheinyl Hydrolase (PptH) from Mycobacterium… · the same entry in another collection · chain D against D, TM-score 1.00
- I6YEE1 · AlphaFold monomer V2.0 prediction for [acyl-carrier-protein] phosphodiesterase ppth… · a predicted model of the same protein · chain A 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 I6YEE1
- Elsewhere: RCSB PDB 6UNC · PDBe 6UNC · UniProt I6YEE1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.