Research workbench
Crystal structure of bifunctional enzyme fold- methylenetetrahydrofolate DEHYDROGENASE/CYCLOHYDROLASE from campylobacter jejuni
Analyse Crystal structure of bifunctional enzyme fold- methylenetetrahydrofolate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DE8
- Type
- protein
- Length
- 564 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional protein fold
- EC
- 1.5.1.5, 3.5.4.9
- UniProt
- Q0PA35
- Ligands
- K, IOD, CL
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bifunctional protein fold (EC 1.5.1.5, 3.5.4.9) | protein | 282 | 44% helix, 17% strand | Q0PA35 |
Ligands and binding sites
- K · Potassium ion · metal · chains B
- IOD · Iodide ion · ion · 17 copies · chains A, B
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.74 | 0.99 | 17 | empty |
| 2 | 399 | 0.65 | 0.79 | 38 | IOD |
| 3 | 479 | 0.65 | 0.77 | 47 | IOD |
| 4 | 56 | 0.62 | 0.92 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1724 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 6DE8 · Crystal Structure of Bifunctional Enzyme FolD-Methylenetetrahydrofolate… · the same entry in another collection · chain A against A, TM-score 1.00
- Q0PA35 · AlphaFold monomer V2.0 prediction for bifunctional protein fold (Q0PA35) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q0PA35
- Elsewhere: RCSB PDB 6DE8 · PDBe 6DE8 · UniProt Q0PA35
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