Research workbench
Crystal structure of pseudomonas aeruginosa lpxa in complex with compound 1
Analyse Crystal structure of pseudomonas aeruginosa lpxa in complex with compound 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OJP
- Type
- protein
- Length
- 7,736 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
- VFE, MG
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, G, H, I, K, L, R, S, T, V, W, Y | Acyl-[acyl-carrier-protein]-udp-N-acetylglucosamine O- acyltransferase (EC 2.3.1.129) | protein | 258 | 18% helix, 28% strand | A6V1E4 |
| C, D, F, J, M, N, O, P, Q, a, b, c | Acyl-[acyl-carrier-protein]-udp-N-acetylglucosamine O- acyltransferase (EC 2.3.1.129) | protein | 257 | 18% helix, 28% strand | A6V1E4 |
| U, X | Acyl-[acyl-carrier-protein]-udp-N-acetylglucosamine O- acyltransferase (EC 2.3.1.129) | protein | 259 | 18% helix, 27% strand | A6V1E4 |
| Z, d | Acyl-[acyl-carrier-protein]-udp-N-acetylglucosamine O- acyltransferase (EC 2.3.1.129) | protein | 261 | 18% helix, 28% strand | A6V1E4 |
Ligands and binding sites
- VFE · 2-[2-(2-chlorophenyl)sulfanylethanoyl-[[4-(1,2,4-triazol-1-yl)phenyl]methyl]amino]-N-methyl-ethanamide · ligand · 30 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d
- MG · Magnesium ion · metal · chains D
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 | 1179 | 0.76 | 0.78 | 93 | VFE |
| 2 | 801 | 0.75 | 0.79 | 69 | VFE |
| 3 | 850 | 0.74 | 0.78 | 89 | VFE |
| 4 | 89 | 0.74 | 0.96 | 18 | empty |
| 5 | 825 | 0.74 | 0.79 | 75 | VFE |
Interfaces
60 interfaces between chains.
- M–Z · 1262 Ų buried · 29 hydrogen bonds · protein-protein
- E–S · 1259 Ų buried · 30 hydrogen bonds · protein-protein
- F–L · 1256 Ų buried · 31 hydrogen bonds · protein-protein
- B–O · 1250 Ų buried · 26 hydrogen bonds · protein-protein
- C–K · 1242 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 7OJP · Crystal structure of Pseudomonas aeruginosa LpxA in complex with compound 1 · the same entry in another collection · chain K against K, 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 7OJP · PDBe 7OJP · UniProt A6V1E4
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