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Structural basis for the sugar nucleotide and acyl chain selectivity of leptospira interrogans lpxa
Analyse Structural basis for the sugar nucleotide and acyl chain selectivity of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I3A
- Type
- protein
- Length
- 777 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
- Q8EZA6
- Ligands
- S2N
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Acyl-[acyl-carrier-protein]--udp-N- acetylglucosamine O-acyltransferase (EC 2.3.1.129) | protein | 259 | 16% helix, 29% strand | Q8EZA6 |
Ligands and binding sites
- S2N · S-[2-({N-[(2R)-2-hydroxy-4-{[(S)-hydroxy(methoxy)phosphoryl]oxy}-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl] (3R)-3-hydroxydodecanethioate · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 700 | 0.76 | 0.81 | 53 | empty |
| 2 | 152 | 0.61 | 0.84 | 27 | empty |
| 3 | 66 | 0.33 | 0.76 | 13 | empty |
| 4 | 58 | 0.31 | 0.76 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 470 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 413 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3I3A · Structural Basis for the Sugar Nucleotide and Acyl Chain Selectivity of Leptospira… · the same entry in another collection · chain A against A, 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 Q8EZA6
- Elsewhere: RCSB PDB 3I3A · PDBe 3I3A · UniProt Q8EZA6
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