MolNFT v1 · #116638 · protein
Crystal structure of LOV2 (C450A) domain in complex with ZDK2
5DJT · NPH1-2: “Crystal structure of LOV2 (C450A) domain in complex with ZDK2”. X-ray diffraction, 3 ligands (FMN, CU, CL), 1 pocket (best druggability 0.69). MolNFT v1 #116638 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DJT
- Type
- protein
- Length
- 203 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NPH1-2; Engineered protein, ZDK2 affibody
- UniProt
- O49004
- Ligands
- FMN, CU, CL
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NPH1-2 | protein | 144 | 35% helix, 27% strand | O49004 |
| B | Engineered protein, ZDK2 affibody | protein | 59 | 69% helix, 0% strand | — |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- CU · Copper (II) ion · metal · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.69 | 0.87 | 25 | FMN, CL |
Interfaces
1 interface between chains.
- A–B · 870 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5DJT · Crystal structure of LOV2 (C450A) domain in complex with Zdk2 · 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 O49004
- Elsewhere: RCSB PDB 5DJT · PDBe 5DJT · UniProt O49004
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