Research workbench
Semet-substituted form of nikd
Analyse Semet-substituted form of nikd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q6U
- Type
- protein
- Length
- 383 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nikd protein
- UniProt
- Q9X9P9
- Ligands
- FAD, BEZ
- Pockets
- 3 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nikd protein | protein | 383 | 30% helix, 28% strand | Q9X9P9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 490 | 0.87 | 0.93 | 62 | FAD, BEZ |
| 2 | 57 | 0.62 | 0.92 | 24 | empty |
| 3 | 81 | 0.51 | 0.84 | 27 | empty |
Modifications
Observed in the structure: 5 modified, 1 cofactor (engineered, flavinylation).
Compared structures
- 2Q6U · SeMet-substituted form of NikD · 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 Q9X9P9
- Elsewhere: RCSB PDB 2Q6U · PDBe 2Q6U · UniProt Q9X9P9
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