Research workbench
Structure of the aquifex aeolicus LPXC/LPC-011 complex
Analyse Structure of the aquifex aeolicus LPXC/LPC-011 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DRO
- 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
- ZH2, ZN
- Pockets
- 6 · 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
- ZH2 · 4-[4-(4-aminophenyl)buta-1,3-diyn-1-yl]-N-[(2S,3R)-3-hydroxy-1-(hydroxyamino)-1-oxobutan-2-yl]benzamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
- ACT · Acetate ion · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.71 | 0.83 | 45 | ZN, ZH2 |
| 2 | 378 | 0.67 | 0.80 | 42 | ZH2, DMS |
| 3 | 114 | 0.42 | 0.76 | 19 | empty |
| 4 | 71 | 0.39 | 0.79 | 18 | empty |
| 5 | 137 | 0.38 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 652 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5DRO · Structure of the Aquifex aeolicus LpxC/LPC-011 Complex · 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 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 O67648
- Elsewhere: RCSB PDB 5DRO · PDBe 5DRO · UniProt O67648
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