Structure of IDP91783
Crystal structure of aminoglycoside 4'-O-adenylyltransferase ANT(4')-IIb, tobramycin-bound
Edit deposit information
- CSGID target
- IDP91783
- PDB Id
- 4EBK (NCBI MMDB)
- Authors
- P.J.Stogios,A.Dong,G.Minasov,E.Evdokimova,O.Egorova,V.Yim,M.Kudritska,P.Courvalin,A.Savchenko,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid)
- Responsible person
- Peter Stogios
- Responsible lab
- University of Calgary
- Deposition Date
- Mar 23, 2012
- Release Date
- Apr 04, 2012
Annotation
- Description
- Resistance to aminoglycoside antibiotics is mediated by chemical modifications: O-phosphorylation (APH enzymes), N-acetylation (AAC enzymes) and N-adenylation (ANT enzymes). In this entry, we present the structure of ANT(4')-IIb, an enzyme which adenylates tobramycin and amikacin antibiotics. The structure is dimeric and contains a nucleotidyltransferase domain. The antibiotic is bound in an electronegative pocket. This is only the second ANT enzyme structure and will be useful to understand the substrate discrimination mechanism and for identification of small molecule inhibitors.
- Functional assignment
- nucleotidyltransferase
Ligands
| Ligand code | Name | Ligand type |
|---|---|---|
| IOD | crystallization | |
| EDO | ethylene diol | crystallization |
| TOY | tobramycin | biological |
| MSE | modified residue | |
| IYR | 3-iodo-tyrosine | modified residue |
| 175 | 3,5-dihydro-5-methylidene-4h-imidazol-4-on |
Structure information
Unit cell parameters
- Space Group
- P 21 21 21
- Unit Cell
-
a=81.91Å, b=84.45Å, c=98.76Å
α=90.00, β=90.00, γ=90.00 - Solvent content
- Matthews coefficient
- Resolution range
- 23.89-2.15Å (2.17-2.15Å)
- Rall(%)
- 17.4
- Rwork(%)
- 17.2 (25.5)
- Rfree(%)
- 22.1 (35.0)
- Num. observed reflections
- 39914 (2355)
- Num. Rfree reflections
- 2111 (130)
- Completeness(%)
- 99.5 (87.0)
- Num Atoms
- 4042
- Num Waters
- 475
- Num Hetatoms
- 686
- Model mean isotropic B factor
- 38.600Å2
- RMSD bond length
- 0.008Å
- RMSD bond angle
- 1.142°
- RMSD dihedral angle
- 13.155°
- Filename uploaded
- 4EBK.pdb (uploaded on Apr 06, 2012 2:03 PM)
- Inserted
- Mar 29, 2012