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Crystal structure of aquifex aeolicus lpxc complexed with uridine 5'- diphosphate
Analyse Crystal structure of aquifex aeolicus lpxc complexed with uridine 5'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IER
- Type
- protein
- Length
- 534 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
- EC
- 3.5.1.-
- UniProt
- O67648
- Ligands
- UDP, PLM, ZN
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-) | protein | 267 | 24% helix, 36% strand | O67648 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- PLM · Palmitic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 9 copies · chains A, B
- 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.71 | 0.81 | 42 | ZN, UDP, PLM |
| 2 | 437 | 0.70 | 0.81 | 44 | ZN, UDP, PLM |
| 3 | 350 | 0.57 | 0.75 | 38 | GOL |
| 4 | 58 | 0.36 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 351 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2IER · Crystal Structure of Aquifex aeolicus LpxC Complexed with Uridine 5'-Diphosphate · the same entry in another collection · chain A against A, TM-score 1.00
- O67648 · AlphaFold monomer V2.0 prediction for udp-3-O-acyl-N- acetylglucosamine deacetylase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O67648
- Elsewhere: RCSB PDB 2IER · PDBe 2IER · UniProt O67648
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