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Crystal structure of putative 2-pyrone-4,6-dicarboxylic acid hydrolase from pseudomonas putida, northeast structural genomics target PPR23.
Analyse Crystal structure of putative 2-pyrone-4,6-dicarboxylic acid hydrolase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FFI
- Type
- protein
- Length
- 546 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-pyrone-4,6-dicarboxylic acid hydrolase, putative
- UniProt
- Q88M75
- Ligands
- PO4
- Pockets
- 8 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-pyrone-4,6-dicarboxylic acid hydrolase, putative | protein | 273 | 41% helix, 11% strand | Q88M75 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.56 | 0.83 | 31 | empty |
| 2 | 131 | 0.52 | 0.81 | 20 | PO4 |
| 3 | 120 | 0.50 | 0.80 | 19 | PO4 |
| 4 | 124 | 0.42 | 0.76 | 18 | empty |
| 5 | 114 | 0.40 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 689 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 2FFI · Crystal Structure of Putative 2-Pyrone-4,6-Dicarboxylic Acid Hydrolase from Pseudomonas… · 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 Q88M75
- Elsewhere: RCSB PDB 2FFI · PDBe 2FFI · UniProt Q88M75
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