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Structure the proline utilization a proline dehydrogenase domain (PUTA86-630) inactivated with N-propargylglycine
Analyse Structure the proline utilization a proline dehydrogenase domain (PUTA86-630)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ITG
- Type
- protein
- Length
- 800 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional protein puta
- EC
- 1.5.99.8, 1.5.1.12
- UniProt
- P09546
- Ligands
- FDA
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional protein puta (EC 1.5.99.8, 1.5.1.12) | protein | 399 | 53% helix, 12% strand | P09546 |
| B | Bifunctional protein puta (EC 1.5.99.8, 1.5.1.12) | protein | 401 | 52% helix, 11% strand | P09546 |
Ligands and binding sites
- FDA · Dihydroflavine-adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 670 | 0.78 | 0.83 | 68 | FDA |
| 2 | 687 | 0.78 | 0.82 | 72 | FDA |
| 3 | 780 | 0.67 | 0.75 | 80 | empty |
| 4 | 236 | 0.56 | 0.78 | 28 | empty |
| 5 | 100 | 0.42 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 722 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 3ITG · Structure the proline utilization A proline dehydrogenase domain (PutA86-630) inactivated… · the same entry in another collection · chain A against A, TM-score 1.00
- P09546 · AlphaFold monomer V2.0 prediction for bifunctional protein puta (P09546) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P09546
- Elsewhere: RCSB PDB 3ITG · PDBe 3ITG · UniProt P09546
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