Research workbench
Crystal structure of the escherichia COLI LPXC/L-161,240 complex
Analyse Crystal structure of the escherichia COLI LPXC/L-161,240 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IS9
- Type
- protein
- Length
- 599 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
- D5CV28
- Ligands
- LTF, ZN, NA
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-) | protein | 300 | 26% helix, 32% strand | D5CV28 |
| B | Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-) | protein | 299 | 24% helix, 32% strand | D5CV28 |
Ligands and binding sites
- LTF · (4R)-2-(3,4-dimethoxy-5-propylphenyl)-N-hydroxy-4,5-dihydro-1,3-oxazole-4-carboxamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal
- IPA · Isopropyl alcohol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.73 | 0.98 | 15 | empty |
| 2 | 924 | 0.69 | 0.74 | 65 | empty |
| 3 | 326 | 0.67 | 0.81 | 41 | LTF |
| 4 | 355 | 0.66 | 0.80 | 46 | LTF |
| 5 | 114 | 0.48 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 691 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4IS9 · Crystal Structure of the Escherichia coli LpxC/L-161,240 complex · 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 D5CV28
- Elsewhere: RCSB PDB 4IS9 · PDBe 4IS9 · UniProt D5CV28
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