Research workbench
Structure of proline utilization a with the FAD covalently modified by L-thiazolidine-2-carboxylate and three cysteines (CYS46, CYS470, CYS638) modified to S,S-(2-HYDROXYETHYL)THIOCYSTEINE
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
- 6UFP
- Type
- protein
- Length
- 2,394 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
- FDA, T2C, NAD, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional protein puta (EC 1.5.5.2, 1.2.1.88) | protein | 1197 | 49% helix, 15% strand | F7X6I3 |
| B | Bifunctional protein puta (EC 1.5.5.2, 1.2.1.88) | protein | 1197 | 49% helix, 15% strand | F7X6I3 |
Ligands and binding sites
- FDA · Dihydroflavine-adenine dinucleotide · ligand · 2 copies · chains A, B
- T2C · (2S)-1,3-thiazolidine-2-carboxylic acid · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- FMT · Formic acid · additive · 2 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 | 778 | 0.86 | 0.89 | 84 | FDA, T2C |
| 2 | 635 | 0.86 | 0.90 | 58 | FDA, T2C |
| 3 | 500 | 0.83 | 0.89 | 89 | empty |
| 4 | 508 | 0.79 | 0.87 | 74 | empty |
| 5 | 1143 | 0.79 | 0.81 | 111 | empty |
Interfaces
1 interface between chains.
- A–B · 1896 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (artifact).
Compared structures
- 6UFP · Structure of proline utilization A with the FAD covalently modified by… · 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 6UFP · PDBe 6UFP · UniProt F7X6I3
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