MolNFT v1 · #116515 · protein
Structure of pseudomonas aeruginosa lpxa in complex with udp-3-O-(R-3- hydroxydecanoyl)-glcnac
5DG3 · Acyl-[acyl-carrier-protein]--udp-N-acetylglucosamine O…: “Structure of pseudomonas aeruginosa lpxa in complex with udp-3-O-(R-3- hydroxydecanoyl)-glcnac”. X-ray diffraction, 2 ligands (U21, PO4), 19 pockets (best druggability 0.77).…
- PDB
- 5DG3
- Type
- protein
- Length
- 1,531 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
- U21, PO4
- Pockets
- 19 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Acyl-[acyl-carrier-protein]--udp-N-acetylglucosamine O- acyltransferase (EC 2.3.1.129) | protein | 256 | 18% helix, 28% strand | A6V1E4 |
| B, F | Acyl-[acyl-carrier-protein]--udp-N-acetylglucosamine O- acyltransferase (EC 2.3.1.129) | protein | 257 | 18% helix, 28% strand | A6V1E4 |
| D | Acyl-[acyl-carrier-protein]--udp-N-acetylglucosamine O- acyltransferase (EC 2.3.1.129) | protein | 249 | 18% helix, 29% strand | A6V1E4 |
Ligands and binding sites
- U21 · uridine-5'-diphosphate-3-O-(R-3-hydroxydecanoyl)-N-acetyl-D-glucosamine · ligand · 4 copies · chains A, B, C, D, E
- PO4 · Phosphate ion · ion · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.77 | 0.79 | 98 | U21 |
| 2 | 1154 | 0.77 | 0.79 | 118 | empty |
| 3 | 646 | 0.74 | 0.81 | 56 | empty |
| 4 | 524 | 0.74 | 0.82 | 50 | empty |
| 5 | 86 | 0.73 | 0.95 | 18 | empty |
Interfaces
9 interfaces between chains.
- A–C · 1055 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 990 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 984 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 793 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 554 Ų buried · 2 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 5DG3 · PDBe 5DG3 · UniProt A6V1E4
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