Download MendeleyStructures of Three New Crystal Forms of the Ykud L,D-Transpeptidase from B. Subtilis.
Blaise, M., Fuglsang Midtgaard, S., Roi Midtgaard, S., Boesen, T., Thirup, S.To be published.
4A1K
Ykud L,D-transpeptidase
- PDB DOI: https://doi.org/10.2210/pdb4A1K/pdb
- Classification: TRANSFERASE
- Organism(s): Bacillus subtilis
- Expression System: Escherichia coli BL21
- Mutation(s): Yes
- Deposited: 2011-09-15 Released: 2012-09-26
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.75 Å
- R-Value Free: 0.212
- R-Value Work: 0.186
- R-Value Observed: 0.188
wwPDB Validation 3D Report Full Report
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 |
| PUTATIVE L, D-TRANSPEPTIDASE YKUD | 165 | Bacillus subtilis | Mutation(s): 2 EC: 2 |  | |
UniProt | |||||
Find proteins for O34816 (Bacillus subtilis (strain 168)) Explore O34816 Go to UniProtKB: O34816 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O34816 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | B [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| CME Query on CME | A | L-PEPTIDE LINKING | C5 H11 N O3 S2 |  | CYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.75 Å
- R-Value Free: 0.212
- R-Value Work: 0.186
- R-Value Observed: 0.188
- Space Group: P 41 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 59.9 | α = 90 |
| b = 59.9 | β = 90 |
| c = 117.75 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
Entry History
Deposition Data
- Released Date: 2012-09-26 Deposition Author(s): Blaise, M., Fuglsang Midtgaard, S., Roi Midtgaard, S., Boesen, T., Thirup, S.
Revision History (Full details and data files)
- Version 1.0: 2012-09-26
Type: Initial release - Version 1.1: 2018-01-17
Changes: Advisory, Data collection - Version 1.2: 2023-12-20
Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description
