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 | pdb_00003k6l
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 (Depositor), 0.310 (DCC)
- R-Value Work: 0.258 (Depositor), 0.250 (DCC)
- R-Value Observed: 0.261 (Depositor)
Starting Model: experimental
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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 | |||||
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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 (Depositor), 0.310 (DCC)
- R-Value Work: 0.258 (Depositor), 0.250 (DCC)
- R-Value Observed: 0.261 (Depositor)
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
