Research workbench
Crystal structure of lkce E64Q mutant in complex with lc-KA05
Analyse Crystal structure of lkce E64Q mutant in complex with lc-KA05 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F7V
- Type
- protein
- Length
- 861 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lkce
- EC
- 1.4.3.4
- UniProt
- G4V2H3
- Ligands
- FAD, CWH, CA
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lkce (EC 1.4.3.4) | protein | 430 | 37% helix, 23% strand | G4V2H3 |
| B | Lkce (EC 1.4.3.4) | protein | 431 | 37% helix, 23% strand | G4V2H3 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- CWH · [(2~{S},5~{R},8~{S},11~{S})-1-[(2~{R},3~{R},5~{R}, 6~{S})-3,5-dimethyl-6-oxidanyl-4-oxidanylidene-oxan-2-yl]-5,11-dimethyl-8-oxidanyl-13-[[(2~{S})-2-oxidanylpropanoyl]amino]tridecan-2-yl] ethanoate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.83 | 0.84 | 85 | FAD, CWH |
| 2 | 929 | 0.83 | 0.84 | 85 | FAD, CWH |
| 3 | 352 | 0.68 | 0.82 | 64 | empty |
| 4 | 298 | 0.61 | 0.79 | 51 | empty |
| 5 | 63 | 0.42 | 0.81 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1376 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6F7V · Crystal structure of LkcE E64Q mutant in complex with LC-KA05 · 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 6F7V · PDBe 6F7V · UniProt G4V2H3
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