MolNFT v1 · #148874 · protein
Crystal structure of the seleniated lkce from streptomyces rochei
6FJH: “Crystal structure of the seleniated lkce from streptomyces rochei”. X-ray diffraction, 3 ligands (FAD, NA, OXY), 9 pockets (best druggability 0.85). MolNFT v1 #148874 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6FJH
- Type
- protein
- Length
- 861 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lkce
- UniProt
- G4V2H3
- Ligands
- FAD, NA, OXY
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lkce | protein | 430 | 36% helix, 22% strand | G4V2H3 |
| B | Lkce | protein | 431 | 34% helix, 23% strand | G4V2H3 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- OXY · Oxygen molecule · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 929 | 0.85 | 0.86 | 83 | FAD, OXY |
| 2 | 890 | 0.84 | 0.85 | 87 | FAD, OXY |
| 3 | 150 | 0.59 | 0.83 | 30 | empty |
| 4 | 141 | 0.52 | 0.80 | 33 | NA |
| 5 | 116 | 0.46 | 0.78 | 25 | NA |
Interfaces
1 interface between chains.
- A–B · 1328 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 6FJH · Crystal structure of the seleniated LkcE from Streptomyces rochei · 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 G4V2H3
- Elsewhere: RCSB PDB 6FJH · PDBe 6FJH · UniProt G4V2H3
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