Download MendeleyStructural basis for the antibacterial activity of the 12-membered-ring mono-sugar macrolide methymycin
Auerbach, T., Mermershtain, I., Bashan, A., Davidovich, C., Rozenberg, H., Sherman, D.H., Yonath, A.(2009) BioTechnologia (Pozn) 1: 24-35
3FWO
The large ribosomal subunit from Deinococcus radiodurans complexed with Methymycin
- PDB DOI: https://doi.org/10.2210/pdb3FWO/pdb
- NAKB: 3FWO
- Classification: RIBOSOME
- Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
- Mutation(s): No
- Deposited: 2009-01-19 Released: 2010-01-19
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.71 Å
- R-Value Free: 0.337
- R-Value Work: 0.278
- R-Value Observed: 0.278
wwPDB Validation 3D Report Full Report
This is version 1.3 of the entry. See complete history.
Literature
Macromolecules
Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| 23S RIBOSOMAL RNA | 2,880 | Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 |  | ||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| 5S RIBOSOMAL RNA | 118 | Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MT9 Query on MT9 | C [auth A] | (3R,4S,5S,7R,9E,11S,12R)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxooxacyclododec-9-en-4-yl 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranoside C25 H43 N O7 HUKYPYXOBINMND-HYUJHOPRSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.71 Å
- R-Value Free: 0.337
- R-Value Work: 0.278
- R-Value Observed: 0.278
- Space Group: I 2 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 172.499 | α = 90 |
| b = 415.691 | β = 90 |
| c = 701.729 | γ = 90 |
| Software Name | Purpose |
|---|---|
| MxCuBE | data collection |
| CNS | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2010-01-19 Deposition Author(s): Auerbach, T., Mermershtain, I., Bashan, A., Davidovich, C., Rozenberg, H., Sherman, D.H., Yonath, A.
Revision History (Full details and data files)
- Version 1.0: 2010-01-19
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2014-02-19
Changes: Database references, Structure summary - Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations
