Download MendeleyThe structure of E.coli peptide deformylase (PDF) in complex with peptidomimetic ligand BB2827
Cheng, R.K.Y., Crawley, L., Wood, M., Barker, J., Felicetti, B., Whittaker, M.To be published.
3K6L
The structure of E.coli peptide deformylase (PDF) in complex with peptidomimetic ligand BB2827
- PDB DOI: https://doi.org/10.2210/pdb3K6L/pdb
- Classification: HYDROLASE
- Organism(s): Escherichia coli K-12
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2009-10-09 Released: 2009-11-10
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.15 Å
- R-Value Free: 0.319
- R-Value Work: 0.258
- R-Value Observed: 0.261
This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Peptide deformylase | 169 | Escherichia coli K-12 | Mutation(s): 0 Gene Names: def, fms, b3287, JW3248 EC: 3.5.1.88 |  | |
UniProt | |||||
Find proteins for P0A6K3 (Escherichia coli (strain K12)) Explore P0A6K3 Go to UniProtKB: P0A6K3 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0A6K3 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 2BB Query on 2BB | E [auth A], G [auth B] | (2S,3R)-N~4~-[(1S)-1-(dimethylcarbamoyl)-2,2-dimethylpropyl]-N~1~,2-dihydroxy-3-(2-methylpropyl)butanediamide C16 H31 N3 O5 USHCFFHZEHRVBD-GRYCIOLGSA-N |  | ||
| NI Query on NI | D [auth A], F [auth B], H [auth C] | NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.15 Å
- R-Value Free: 0.319
- R-Value Work: 0.258
- R-Value Observed: 0.261
- Space Group: P 43 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 73.96 | α = 90 |
| b = 73.96 | β = 90 |
| c = 241.5 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DNA | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
Entry History
Deposition Data
- Released Date: 2009-11-10 Deposition Author(s): Cheng, R.K.Y., Crawley, L., Wood, M., Barker, J., Felicetti, B., Whittaker, M.
Revision History (Full details and data files)
- Version 1.0: 2009-11-10
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
