Research workbench
Crystal structure of aminoglycoside 4'-O-adenylyltransferase ANT(4')- iib, tobramycin-bound
Analyse Crystal structure of aminoglycoside 4'-O-adenylyltransferase ANT(4')- iib… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EBK
- Type
- protein
- Length
- 513 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminoglycoside nucleotidyltransferase
- UniProt
- Q83V96
- Ligands
- TOY, CL, IOD
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminoglycoside nucleotidyltransferase | protein | 257 | 52% helix, 19% strand | Q83V96 |
| B | Aminoglycoside nucleotidyltransferase | protein | 256 | 52% helix, 20% strand | Q83V96 |
Ligands and binding sites
- TOY · Tobramycin · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 17 copies · chains A, B
- IOD · Iodide ion · ion · 12 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.80 | 0.82 | 104 | TOY, IOD, CL |
| 2 | 71 | 0.39 | 0.78 | 14 | IOD, CL |
| 3 | 76 | 0.38 | 0.78 | 13 | IOD, CL |
| 4 | 56 | 0.37 | 0.80 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2515 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered, nonstandard).
Compared structures
- 4EBK · Crystal structure of aminoglycoside 4'-O-adenylyltransferase ANT(4')-IIb, tobramycin-bound · 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 Q83V96
- Elsewhere: RCSB PDB 4EBK · PDBe 4EBK · UniProt Q83V96
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