Research workbench
Crystal structure of pseudomonas aeruginosa lpxa in complex with compound 14
Analyse Crystal structure of pseudomonas aeruginosa lpxa in complex with compound 14 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OKA
- Type
- protein
- Length
- 7,725 residues
- Chains
- 30
- 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
- VFT, SO4, CL
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, J, K, L, S, T, U, Y, Z, c | Acyl-[acyl-carrier-protein]-udp-N-acetylglucosamine O- acyltransferase (EC 2.3.1.129) | protein | 258 | 18% helix, 28% strand | A6V1E4 |
| G, H, I, M, N, O, P, Q, R, V, W, X, a, b, d | Acyl-[acyl-carrier-protein]-udp-N-acetylglucosamine O- acyltransferase (EC 2.3.1.129) | protein | 257 | 18% helix, 28% strand | A6V1E4 |
Ligands and binding sites
- VFT · 2-(2-chlorophenyl)sulfanyl-~{N}-[(4-cyanophenyl) methyl]-~{N}-(1~{H}-imidazol-4-ylmethyl)ethanamide · ligand · 30 copies · chains A, C, B, D, E, F, G, H, I, M, N, O, J, K, L, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, d, c
- SO4 · Sulfate ion · ion · 71 copies · chains A, B, C, D, E, F, G, H, I, M, N, O, J, K, L, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d
- CL · Chloride ion · ion · 21 copies · chains A, B, C, D, E, F, G, I, M, N, O, L, Q, S, T, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 780 | 0.76 | 0.81 | 94 | VFT, SO4 |
| 2 | 986 | 0.76 | 0.78 | 90 | SO4, VFT |
| 3 | 972 | 0.76 | 0.79 | 81 | VFT, SO4 |
| 4 | 712 | 0.76 | 0.81 | 79 | VFT, SO4 |
| 5 | 914 | 0.75 | 0.79 | 76 | VFT, SO4 |
Interfaces
66 interfaces between chains.
- F–P · 1267 Ų buried · 24 hydrogen bonds · protein-protein
- B–O · 1250 Ų buried · 30 hydrogen bonds · protein-protein
- A–a · 1240 Ų buried · 28 hydrogen bonds · protein-protein
- E–I · 1238 Ų buried · 26 hydrogen bonds · protein-protein
- K–R · 1235 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 7OKA · Crystal structure of Pseudomonas aeruginosa LpxA in complex with compound 14 · the same entry in another collection · chain N against N, 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 A6V1E4
- Elsewhere: RCSB PDB 7OKA · PDBe 7OKA · UniProt A6V1E4
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