MolNFT v1 · #190001 · protein
Crystal structure of gigantea in complex with LKP2
7WA4 · Protein gigantea: “Crystal structure of gigantea in complex with LKP2”. X-ray diffraction, 1 ligand (FMN), 5 pockets (best druggability 0.76). MolNFT v1 #190001 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7WA4
- Type
- protein
- Length
- 636 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein gigantea; Adagio protein 2
- UniProt
- Q9SQI2, Q8W420
- Ligands
- FMN
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein gigantea | protein | 529 | 73% helix, 0% strand | Q9SQI2 |
| B | Adagio protein 2 | protein | 107 | 25% helix, 39% strand | Q8W420 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.76 | 0.91 | 26 | FMN |
| 2 | 149 | 0.44 | 0.75 | 19 | empty |
| 3 | 53 | 0.37 | 0.80 | 16 | empty |
| 4 | 96 | 0.36 | 0.74 | 15 | empty |
| 5 | 55 | 0.28 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 927 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 modified, 1 cofactor (engineered, flavinylation).
Compared structures
- 7WA4 · Crystal structure of GIGANTEA in complex with LKP2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q8W420 · AlphaFold monomer V2.0 prediction for adagio protein 2 (Q8W420) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q9SQI2 · AlphaFold monomer V2.0 prediction for protein gigantea (Q9SQI2) · a predicted model of the same protein · chain A against A, TM-score 0.76
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 Q9SQI2
- Every structure of UniProt Q8W420
- Elsewhere: RCSB PDB 7WA4 · PDBe 7WA4 · UniProt Q9SQI2 · UniProt Q8W420
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