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Crystal structure of the 3-N-acetyl transferase wlbb from bordetella petrii in complex with CoA and udp-3-amino-2-acetamido-2,3-dideoxy glucuronic acid
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
- 3MQH
- Type
- protein
- Length
- 1,146 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
- MJZ, COA, NA, PO4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 2% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipopolysaccharides biosynthesis acetyltransferase (EC 2.3.1.-) | protein | 191 | 2% helix, 36% strand | A9IH93 |
| B | Lipopolysaccharides biosynthesis acetyltransferase (EC 2.3.1.-) | protein | 189 | 2% helix, 37% strand | A9IH93 |
| C, D, E | Lipopolysaccharides biosynthesis acetyltransferase (EC 2.3.1.-) | protein | 192 | 2% helix, 35% strand | A9IH93 |
| F | Lipopolysaccharides biosynthesis acetyltransferase (EC 2.3.1.-) | protein | 190 | 2% helix, 36% strand | A9IH93 |
Ligands and binding sites
- MJZ · (2S,3S,4R,5R,6R)-5-(acetylamino)-4-amino-6-{[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3-hydroxytetrahydro-2H-pyran-2-carboxylic acid · ligand · 6 copies · chains A, C, B, D, F, E
- COA · Coenzyme A · ligand · 6 copies · chains A, B, C, D, E, F
- 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 · 12 copies · chains A, B, C, D, E, F
- 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 | 571 | 0.76 | 0.83 | 59 | COA, EDO, MJZ |
| 2 | 551 | 0.76 | 0.83 | 56 | MJZ, COA, EDO |
| 3 | 542 | 0.75 | 0.83 | 56 | COA, EDO, MJZ |
| 4 | 539 | 0.75 | 0.82 | 60 | MJZ, COA, EDO |
| 5 | 530 | 0.74 | 0.82 | 57 | COA, EDO, MJZ |
Interfaces
9 interfaces between chains.
- A–B · 1169 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1161 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1158 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 1150 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1144 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3MQH · 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 3MQH · PDBe 3MQH · UniProt A9IH93
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