Research workbench
Lnmk in complex with 2-nitronate-propionyl-CoA
Analyse Lnmk in complex with 2-nitronate-propionyl-CoA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X7L
- Type
- protein
- Length
- 304 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional methylmalonyl-COA:ACP ACYLTRANSFERASE/DECARBOXYLASE
- UniProt
- Q8GGP1
- Ligands
- KFV, SO4
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional methylmalonyl-COA:ACP ACYLTRANSFERASE/DECARBOXYLASE | protein | 304 | 24% helix, 36% strand | Q8GGP1 |
Ligands and binding sites
- KFV · [1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-1-oxidanylidene-propan-2-ylidene]-bis(oxidanidyl)azanium · ligand · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.65 | 0.84 | 32 | empty |
| 2 | 263 | 0.63 | 0.81 | 36 | KFV |
| 3 | 55 | 0.26 | 0.73 | 15 | SO4 |
Compared structures
- 6X7L · LnmK in complex with 2-nitronate-propionyl-CoA · 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 Q8GGP1
- Elsewhere: RCSB PDB 6X7L · PDBe 6X7L · UniProt Q8GGP1
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