Research workbench
Crystal structure of haliscomenobacter hydrossis iodotyrosine deiodinase (iyd) bound to FMN and 2-iodophenol (2IP)
Analyse Crystal structure of haliscomenobacter hydrossis iodotyrosine deiodinase (iyd)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KRD
- Type
- protein
- Length
- 401 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitroreductase
- UniProt
- F4KU78
- Ligands
- FMN, 6X8
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitroreductase | protein | 200 | 41% helix, 18% strand | F4KU78 |
| B | Nitroreductase | protein | 201 | 39% helix, 17% strand | F4KU78 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- 6X8 · 2-iodanylphenol · ligand · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.65 | 0.77 | 51 | empty |
| 2 | 190 | 0.56 | 0.80 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 604 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5KRD · Crystal structure of haliscomenobacter hydrossis iodotyrosine deiodinase (IYD) bound to… · 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 F4KU78
- Elsewhere: RCSB PDB 5KRD · PDBe 5KRD · UniProt F4KU78
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