Research workbench
Structure of pseudomonas aeruginosa lpxa in complex with udp-glcnac
Analyse Structure of pseudomonas aeruginosa lpxa in complex with udp-glcnac in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DEP
- Type
- protein
- Length
- 1,542 residues
- Chains
- 6
- 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
- UD1, PO4
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Acyl-[acyl-carrier-protein]--udp-N-acetylglucosamine O- acyltransferase (EC 2.3.1.129) | protein | 258 | 19% helix, 28% strand | A6V1E4 |
| B, E | Acyl-[acyl-carrier-protein]--udp-N-acetylglucosamine O- acyltransferase (EC 2.3.1.129) | protein | 257 | 18% helix, 28% strand | A6V1E4 |
| C, F | Acyl-[acyl-carrier-protein]--udp-N-acetylglucosamine O- acyltransferase (EC 2.3.1.129) | protein | 256 | 18% helix, 28% strand | A6V1E4 |
Ligands and binding sites
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · 6 copies · chains A, B, D, E, F
- PO4 · Phosphate ion · ion · 4 copies · chains B, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.75 | 0.84 | 65 | empty |
| 2 | 657 | 0.72 | 0.79 | 67 | PO4, UD1 |
| 3 | 77 | 0.72 | 0.96 | 18 | empty |
| 4 | 665 | 0.71 | 0.78 | 70 | UD1 |
| 5 | 221 | 0.70 | 0.86 | 31 | PO4 |
Interfaces
8 interfaces between chains.
- D–E · 1028 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1023 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1021 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1021 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1010 Ų buried · 10 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 5DEP · PDBe 5DEP · UniProt A6V1E4
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