Research workbench
Crystal structure of LOV2 (C450A) domain in complex with ZDK3
Analyse Crystal structure of LOV2 (C450A) domain in complex with ZDK3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DJU
- Type
- protein
- Length
- 400 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Engineered protein, ZDK3 affibody; NPH1-2
- UniProt
- O49004
- Ligands
- FMN, CL
- Pockets
- 2 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | Engineered protein, ZDK3 affibody | protein | 55 | 73% helix, 0% strand | — |
| A, C | NPH1-2 | protein | 145 | 39% helix, 27% strand | O49004 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, C
- CL · Chloride ion · ion · 5 copies · chains B, A, D, C
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 | 745 | 0.82 | 0.86 | 67 | FMN, CL |
| 2 | 726 | 0.67 | 0.75 | 50 | empty |
Interfaces
4 interfaces between chains.
- D–C · 1067 Ų buried · 11 hydrogen bonds · protein-protein
- B–A · 1037 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 362 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 12 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5DJU · Crystal structure of LOV2 (C450A) domain in complex with Zdk3 · the same entry in another collection · chain B against B, 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 O49004
- Elsewhere: RCSB PDB 5DJU · PDBe 5DJU · UniProt O49004
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