Research workbench
Structure of proline utilization a with the FAD covalently-modified by 1,3-dithiolane
Analyse Structure of proline utilization a with the FAD covalently-modified by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MYA
- Type
- protein
- Length
- 2,434 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
- UJJ, NAD, MG, SO4
- Pockets
- 20 · best druggability 0.86
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 | 1217 | 49% helix, 15% strand | F7X6I3 |
Ligands and binding sites
- UJJ · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[5-(1,3-dithiolan-2-yl)-7,8-dimethyl-2,4-dioxo-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate · 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 · 7 copies · chains A, B
- PGE · Triethylene glycol · additive · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 651 | 0.86 | 0.90 | 85 | UJJ |
| 2 | 448 | 0.85 | 0.92 | 47 | UJJ |
| 3 | 664 | 0.84 | 0.88 | 106 | NAD, PEG |
| 4 | 337 | 0.81 | 0.91 | 64 | NAD |
| 5 | 1082 | 0.80 | 0.81 | 105 | empty |
Interfaces
1 interface between chains.
- A–B · 1899 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 7MYA · Structure of proline utilization A with the FAD covalently-modified by 1,3-dithiolane · 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 7MYA · PDBe 7MYA · UniProt F7X6I3
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