Research workbench
Crystal structure of pseudomonas aeruginosa lpxa in complex with compound 7
Analyse Crystal structure of pseudomonas aeruginosa lpxa in complex with compound 7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OJQ
- Type
- protein
- Length
- 762 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-[acyl-carrier-protein]--udp-N-acetylglucosamine O- acyltransferase
- EC
- 2.3.1.129
- UniProt
- A6V1E4
- Ligands
- VJE
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-[acyl-carrier-protein]--udp-N-acetylglucosamine O- acyltransferase (EC 2.3.1.129) | protein | 255 | 18% helix, 27% strand | A6V1E4 |
| B | Acyl-[acyl-carrier-protein]--udp-N-acetylglucosamine O- acyltransferase (EC 2.3.1.129) | protein | 252 | 18% helix, 29% strand | A6V1E4 |
| C | Acyl-[acyl-carrier-protein]--udp-N-acetylglucosamine O- acyltransferase (EC 2.3.1.129) | protein | 255 | 18% helix, 29% strand | A6V1E4 |
Ligands and binding sites
- VJE · 2-(2-chlorophenyl)sulfanyl-~{N}-[(4-cyanophenyl) methyl]-~{N}-[(5-methyl-1,3,4-oxadiazol-2-yl) methyl]ethanamide · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.73 | 0.95 | 19 | empty |
| 2 | 398 | 0.64 | 0.78 | 44 | VJE |
| 3 | 310 | 0.60 | 0.78 | 41 | VJE |
| 4 | 338 | 0.60 | 0.77 | 49 | VJE |
| 5 | 240 | 0.49 | 0.74 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–C · 963 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 953 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 907 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
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 A6V1E4
- Elsewhere: RCSB PDB 7OJQ · PDBe 7OJQ · UniProt A6V1E4
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