Research workbench
First structure of a proline utilization a proline dehydrogenase domain
Analyse First structure of a proline utilization a proline dehydrogenase domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O8A
- Type
- protein
- Length
- 462 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional protein puta
- EC
- 1.5.99.8, 1.2.1.88
- UniProt
- P09546
- Ligands
- FAD, 2OP
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional protein puta (EC 1.5.99.8, 1.2.1.88) | protein | 462 | 57% helix, 10% strand | P09546 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- 2OP · (2S)-2-hydroxypropanoic acid · ligand · chains A
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.83 | 0.90 | 42 | FAD, 2OP |
| 2 | 159 | 0.50 | 0.78 | 22 | empty |
| 3 | 70 | 0.32 | 0.75 | 21 | empty |
| 4 | 58 | 0.31 | 0.75 | 15 | empty |
| 5 | 53 | 0.29 | 0.75 | 11 | empty |
Compared structures
- 4O8A · First structure of a proline utilization A proline dehydrogenase domain · 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 0.89
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 4O8A · PDBe 4O8A · UniProt P09546
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