Research workbench
Crystal structure of bradyrhizobium japonicum proline utilization a (puta) mutant D779W
Analyse Crystal structure of bradyrhizobium japonicum proline utilization a (puta)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q71
- Type
- protein
- Length
- 1,942 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline dehydrogenase
- EC
- 1.5.99.8, 1.2.1.88
- UniProt
- Q89E26
- Ligands
- FAD, SO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline dehydrogenase (EC 1.5.99.8, 1.2.1.88) | protein | 972 | 51% helix, 14% strand | Q89E26 |
| B | Proline dehydrogenase (EC 1.5.99.8, 1.2.1.88) | protein | 970 | 51% helix, 14% strand | Q89E26 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.89 | 0.91 | 126 | SO4, GOL |
| 2 | 887 | 0.88 | 0.91 | 135 | SO4 |
| 3 | 542 | 0.86 | 0.91 | 43 | FAD |
| 4 | 652 | 0.85 | 0.90 | 43 | FAD |
| 5 | 747 | 0.74 | 0.79 | 103 | empty |
Interfaces
1 interface between chains.
- A–B · 3400 Ų buried · 69 hydrogen bonds · protein-protein
Compared structures
- 4Q71 · Crystal Structure of Bradyrhizobium japonicum Proline Utilization A (PutA) Mutant D779W · 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 Q89E26
- Elsewhere: RCSB PDB 4Q71 · PDBe 4Q71 · UniProt Q89E26
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