Download MendeleyCrystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli in complex with UMA and two inhibitor A19 molecules
Liu, L., Seibold, S., Lovell, S., Battaile, K.P.To be published.
9BN9
Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli in complex with UMA and two inhibitor A19 molecules
- PDB DOI: https://doi.org/10.2210/pdb9BN9/pdb
- Classification: LIGASE/LIGASE INHIBITOR
- Organism(s): Escherichia coli K-12
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2024-05-02 Released: 2024-05-15
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.23 ?
- R-Value Free: 0.142
- R-Value Work: 0.123
- R-Value Observed: 0.124
Starting Model: experimental
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This is version 1.0 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 |
| UDP-N-acetylmuramoylalanine--D-glutamate ligase | 445 | Escherichia coli K-12 | Mutation(s): 0 Gene Names: murD, b0088, JW0086 EC: 6.3.2.9 |  | |
UniProt | |||||
Find proteins for P14900 (Escherichia coli (strain K12)) Explore P14900 Go to UniProtKB: P14900 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P14900 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| UMA Query on UMA | B [auth A] | URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE C23 H36 N4 O20 P2 NTMMCWJNQNKACG-KBKUWGQMSA-N |  | ||
| A1AQS (Subject of Investigation/LOI) Query on A1AQS | C [auth A], D [auth A] | N-(4-{[(4S)-3-amino[1,2,4]triazolo[4,3-b]pyridazin-6-yl]sulfanyl}phenyl)acetamide C13 H12 N6 O S DDVAGHQEXKJINC-UHFFFAOYSA-N |  | ||
| SO4 Query on SO4 | E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | M [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| CL Query on CL | K [auth A], L [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| KCX Query on KCX | A | L-PEPTIDE LINKING | C7 H14 N2 O4 |  | LYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.23 ?
- R-Value Free: 0.142
- R-Value Work: 0.123
- R-Value Observed: 0.124
- Space Group: P 41
- Diffraction Data: https://doi.org/10.18430/m39bn9
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 65.381 | ¦Á = 90 |
| b = 65.381 | ¦Â = 90 |
| c = 134.681 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| Aimless | data scaling |
| XDS | data reduction |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-05-15 Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | 75N93022C00036 |
| National Institutes of Health/Office of the Director | United States | S10OD030394 |
Revision History (Full details and data files)
- Version 1.0: 2024-05-15
Type: Initial release
