MolNFT v1 · #104322 · protein
Crystal structure of bradyrhizobium japonicum proline utilization a (puta) mutant D779Y
4Q72 · Proline dehydrogenase: “Crystal structure of bradyrhizobium japonicum proline utilization a (puta) mutant D779Y”. X-ray diffraction, 2 ligands (FAD, SO4), 20 pockets (best druggability 0.89). MolNFT v1 #104322 on GenesisL1: 3D…
- PDB
- 4Q72
- Type
- protein
- Length
- 1,940 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 · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline dehydrogenase (EC 1.5.99.8, 1.2.1.88) | protein | 971 | 50% helix, 14% strand | Q89E26 |
| B | Proline dehydrogenase (EC 1.5.99.8, 1.2.1.88) | protein | 969 | 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 · 3 copies · chains A
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 | 981 | 0.89 | 0.91 | 152 | SO4 |
| 2 | 935 | 0.88 | 0.90 | 130 | SO4 |
| 3 | 633 | 0.86 | 0.90 | 42 | FAD |
| 4 | 538 | 0.86 | 0.91 | 43 | FAD |
| 5 | 73 | 0.70 | 0.96 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 3414 Ų buried · 70 hydrogen bonds · protein-protein
Compared structures
- 4Q72 · Crystal Structure of Bradyrhizobium japonicum Proline Utilization A (PutA) Mutant D779Y · 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 4Q72 · PDBe 4Q72 · UniProt Q89E26
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.