Research workbench
Crystal structure of pseudomonas aeruginosa lpxa in complex with compound 3
Analyse Crystal structure of pseudomonas aeruginosa lpxa in complex with compound 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OK1
- Type
- protein
- Length
- 765 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
- VFN, CL
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 28% 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 | 258 | 17% helix, 28% strand | A6V1E4 |
| B | Acyl-[acyl-carrier-protein]-udp-N-acetylglucosamine O- acyltransferase (EC 2.3.1.129) | protein | 254 | 18% helix, 28% strand | A6V1E4 |
| C | Acyl-[acyl-carrier-protein]-udp-N-acetylglucosamine O- acyltransferase (EC 2.3.1.129) | protein | 253 | 18% helix, 28% strand | A6V1E4 |
Ligands and binding sites
- VFN · ~{N}-[(5-azanyl-1,3,4-oxadiazol-2-yl)methyl]-2-(2-chlorophenyl)sulfanyl-~{N}-[(4-cyanophenyl) methyl]ethanamide · ligand · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.71 | 0.95 | 17 | empty |
| 2 | 574 | 0.68 | 0.78 | 67 | VFN, CL |
| 3 | 320 | 0.61 | 0.78 | 41 | VFN, CL |
| 4 | 342 | 0.60 | 0.77 | 40 | VFN |
| 5 | 207 | 0.48 | 0.75 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1013 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 946 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 935 Ų buried · 13 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 7OK1 · PDBe 7OK1 · UniProt A6V1E4
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