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Structure of proline utilization a with 1,3-dithiolane-2-carboxylate bound in the proline dehydrogenase active site
Analyse Structure of proline utilization a with 1,3-dithiolane-2-carboxylate bound in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MY9
- Type
- protein
- Length
- 2,432 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional protein puta
- EC
- 1.5.5.2, 1.2.1.88
- UniProt
- F7X6I3
- Ligands
- UJD, FAD, NAD, MG, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bifunctional protein puta (EC 1.5.5.2, 1.2.1.88) | protein | 1216 | 49% helix, 15% strand | F7X6I3 |
Ligands and binding sites
- UJD · 1,3-dithiolane-2-carboxylic acid · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- PGE · Triethylene glycol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 563 | 0.87 | 0.92 | 55 | UJD, FAD |
| 2 | 665 | 0.87 | 0.91 | 64 | UJD, FAD |
| 3 | 758 | 0.85 | 0.88 | 114 | NAD |
| 4 | 632 | 0.84 | 0.88 | 113 | PEG, NAD |
| 5 | 1003 | 0.82 | 0.83 | 106 | empty |
Interfaces
1 interface between chains.
- A–B · 1832 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 7MY9 · Structure of proline utilization A with 1,3-dithiolane-2-carboxylate bound in the proline… · 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 F7X6I3
- Elsewhere: RCSB PDB 7MY9 · PDBe 7MY9 · UniProt F7X6I3
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