Research workbench
Crystal structure of arsn, N-acetyltransferase with substrate ast from pseudomonas putida KT2440
Analyse Crystal structure of arsn, N-acetyltransferase with substrate ast from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WPH
- Type
- protein
- Length
- 1,070 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphinothricin N-acetyltransferase
- UniProt
- Q88LK7
- Ligands
- BLJ, NA
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F | Phosphinothricin N-acetyltransferase | protein | 179 | 32% helix, 33% strand | Q88LK7 |
| C | Phosphinothricin N-acetyltransferase | protein | 177 | 32% helix, 33% strand | Q88LK7 |
| D, E | Phosphinothricin N-acetyltransferase | protein | 178 | 33% helix, 33% strand | Q88LK7 |
Ligands and binding sites
- BLJ · (2S)-2-amino-4-[hydroxy(methyl)arsoryl]butanoic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B, C, F, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.81 | 0.82 | 129 | empty |
| 2 | 899 | 0.80 | 0.82 | 111 | NA |
| 3 | 939 | 0.80 | 0.82 | 101 | BLJ |
| 4 | 160 | 0.48 | 0.77 | 19 | empty |
| 5 | 129 | 0.46 | 0.78 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1769 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 1736 Ų buried · 24 hydrogen bonds · protein-protein
- C–F · 1731 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 667 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 215 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5WPH · Crystal structure of ArsN, N-acetyltransferase with substrate AST from Pseudomonas putida… · 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 Q88LK7
- Elsewhere: RCSB PDB 5WPH · PDBe 5WPH · UniProt Q88LK7
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