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Crystal structure of the 3-N-acetyl transferase wlbb from bordetella petrii in complex with acetyl-CoA
Analyse Crystal structure of the 3-N-acetyl transferase wlbb from bordetella petrii in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MQG
- Type
- protein
- Length
- 1,143 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipopolysaccharides biosynthesis acetyltransferase
- EC
- 2.3.1.-
- UniProt
- A9IH93
- Ligands
- ACO, UDP, U5P, NA, PO4
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Lipopolysaccharides biosynthesis acetyltransferase (EC 2.3.1.-) | protein | 190 | 2% helix, 36% strand | A9IH93 |
| C, D | Lipopolysaccharides biosynthesis acetyltransferase (EC 2.3.1.-) | protein | 192 | 2% helix, 34% strand | A9IH93 |
| F | Lipopolysaccharides biosynthesis acetyltransferase (EC 2.3.1.-) | protein | 189 | 2% helix, 37% strand | A9IH93 |
Ligands and binding sites
- ACO · Acetyl coenzyme *A · ligand · 6 copies · chains A, B, C, D, E, F
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, F, E
- U5P · Uridine-5'-monophosphate · ligand · 3 copies · chains A, C, D, F, E
- NA · Sodium ion · metal · 2 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 2 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 4 copies · chains B, C, D
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 566 | 0.75 | 0.82 | 54 | ACO, UDP |
| 2 | 536 | 0.75 | 0.82 | 56 | ACO, UDP |
| 3 | 575 | 0.74 | 0.81 | 62 | ACO, U5P |
| 4 | 544 | 0.73 | 0.81 | 60 | U5P, ACO |
| 5 | 537 | 0.72 | 0.80 | 56 | U5P, ACO |
Interfaces
9 interfaces between chains.
- B–C · 1164 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1155 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 1149 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1105 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1103 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3MQG · crystal structure of the 3-N-acetyl transferase WlbB from Bordetella petrii in complex… · 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 A9IH93
- Elsewhere: RCSB PDB 3MQG · PDBe 3MQG · UniProt A9IH93
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