Research workbench
Crystal structure of "apo" form lpxk from aquifex aeolicus in complex with ATP at 2.2 ångström resolution
Analyse Crystal structure of "apo" form lpxk from aquifex aeolicus in complex with ATP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ITM
- Type
- protein
- Length
- 315 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetraacyldisaccharide 4'-kinase
- EC
- 2.7.1.130
- UniProt
- O67572
- Ligands
- ATP
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tetraacyldisaccharide 4'-kinase (EC 2.7.1.130) | protein | 315 | 30% helix, 26% strand | O67572 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.75 | 0.80 | 60 | ATP, MPD, GOL |
| 2 | 169 | 0.48 | 0.76 | 23 | empty |
| 3 | 70 | 0.31 | 0.75 | 14 | EPE |
| 4 | 61 | 0.29 | 0.74 | 11 | empty |
Compared structures
- 4ITM · Crystal structure of apo" form LpxK from Aquifex aeolicus in complex with ATP at 2.2… · the same entry in another collection · chain A against A, TM-score 1.00
- O67572 · AlphaFold monomer V2.0 prediction for tetraacyldisaccharide 4'-kinase (O67572) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 O67572
- Elsewhere: RCSB PDB 4ITM · PDBe 4ITM · UniProt O67572
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.