Download MendeleyCrystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli (ADP bound)
Seibold, S., Lovell, S., Liu, L., Battaile, K.P.To be published.
8VW1
Crystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli (ADP bound)
- PDB DOI: https://doi.org/10.2210/pdb8VW1/pdb
- Classification: LIGASE
- Organism(s): Escherichia coli K-12
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2024-01-31 Released: 2024-02-14
- 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: 1.70 Å
- R-Value Free: 0.197
- R-Value Work: 0.163
- R-Value Observed: 0.164
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 | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ADP (Subject of Investigation/LOI) Query on ADP | B [auth A] | ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N |  | ||
| MPD Query on MPD | I [auth A] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | ||
| DMS Query on DMS | J [auth A] | DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N |  | ||
| CA Query on CA | F [auth A], G [auth A], H [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| MG Query on MG | C [auth A], D [auth A], E [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| 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: 1.70 Å
- R-Value Free: 0.197
- R-Value Work: 0.163
- R-Value Observed: 0.164
- Space Group: P 21 21 21
- Diffraction Data: https://doi.org/10.18430/M38VW1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 58.47 | α = 90 |
| b = 69.235 | β = 90 |
| c = 100.468 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| Aimless | data scaling |
| XDS | data reduction |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-02-14 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: 2024-02-14
Type: Initial release
