PDB and Fragalysis

PDB Codes

These are the PDB codes relevant to this project with a short description of the organism, enzyme, and any ligands bound. Associated discussions in this Github repository (e.g., #67) can be found by searching on the PDB codes or the tag "structural biology".

MurC:

1GQQ: Haemophilus influenzae MurC, Apo

1GQY: Haemophilus influenzae MurC with AMPPCP

1P31: Haemophilus influenzae MurC

1P3D: Haemophilus influenzae MurC with UMA and ANP

2F00: Escherichia coli MurC

4HV4: Yersinia pestis CO92 MurC with AMP

6CAU: Acinetobacter baumannii AB5075-UW with AMPPNP

6X9F: Pseudomonas aeruginosa MurC with AZ8074 (AZcompound 1)

6X9N: Pseudomonas aeruginosa MurC with AZ5595 (AZcompound 10, WYH25-1-P, OSA_001071)

7BVA: Mycobacterium bovis MurC

7BVB: Mycobacterium bovis MurC with UDP-GlcNAc

8DOF: Pseudomonas aeruginosa MurC with OSA_001044 (AZcompound 4, WYH9-2-P)

8EGM: Pseudomonas aeruginosa MurC with AZ-13644908 (AZcompound 22)

8EGN: Pseudomonas aeruginosa MurC with AZ-13643701 (AZcompound 13)

8EWA: Pseudomonas aeruginosa MurC with AZ-13644923 (AZcompound 26)

9D9K: Pseudomonas aeruginosa PAO1 MurC with Inhibitor M17

9D9M: Pseudomonas aeruginosa PAO1 MurC with Sulfate

**Compounds with "AZcompound xx numbering" can be found in the Hameed Paper **Compounds with "AZ-xxxxxx numbering is a internal numbering

MurD:

1E0D: E. coli MurD (Open Structure)

1EEH: E. coli MurD with UMA (Closed Structure)

2UAG: E. coli MurD with ADP + UMA

3UAG: E. coli MurD with ADP + UMA

4UAG: E. coli MurD with ADP + UAG

5A5E: E. coli K12 MurD

5A5F: E. coli K12 MurD with ADP + UMA

7SY9: Pseudomonas aeruginosa MurD PAO1

7TI7: Acinetobacter baumannii MurD AB5075-UW in complex with ADP

7U35: Pseudomonas aeruginosa MurD PAO1 in complex with ADP

8DP2: Pseudomonas aeruginosa MurD PAO1 with UMA

[XXXX in progress](Scott Protein Structure and X-Ray Crystallography Laboratory University of Kansas): Pseudomonas aeruginosa MurD with OSA_001044 (AZcompound 4, WYH9-2-P)

MurE:

1E8C: E. coli MurE with substrate UAG

2XJA : M. tuburculosis MurE with ADP + substrate

7B53: MurE from E.coli, Apo

7B60: MurE from E.coli in complex with Z1269139261

7B61: MurE from E.coli in complex with Z287256168

7B6Q: MurE from E.coli in complex with Z57299526

7B68: MurE from E.coli in complex with Z2856434929

7B6G: MurE from E.coli in complex with Z1675346324

7B9E: MurE from E.coli in complex with Z275151340

7B6I: E.coli MurE in complex with Z1373445602

7B6K: E.coli MurE in complex with Z57715447

7B6J: E.coli MurE in complex with minifrag succinimide

7B6L: E.coli MurE in complex with Z57299368

7B6M: E.coli MurE with Z1198948504

7B9W: E.coli MurE with Z757284952

7B6N: E.coli MurE C269S C340S C450S mutant

7B6O: E.coli MurE in complex with ebselen

7B6P: E.coli MurE C269S C340S C450S mutant in complex with Elman's reagent

7D27: Acinetobacter baumannii MurE, Apo, Open Conformation

4ZIY: Acinetobacter baumannii MurE with ANP

8G6P: Mycolicibacterium thermoresistibile with ADP and 2,6-Diaminopimelic acid

2WTZ: Mycobacterium Tuberculosis MurE with UAG

2XJA: Mycobacterium Tuberculosis MurE with ADP + UAG

MurF:

4CVK: Pae PAO1 MurF with UDP-MurNAc-tripeptide (mDAP)

4CVM: Pae PAO1 MurF with AMP-PNP and UDP-MurNAc-tripeptide (mDAP)

4QF5: Acinetobacter baumannii with ATP

4QDI: Acinetobacter baumannii with ATP + UDP

PDB Files

The PDB files of original hits bound to MurD and MurE are available to download.

Diamond fragalysis pages

MurD: https://fragalysis.diamond.ac.uk/viewer/react/preview/target/MURD

MurE: https://fragalysis.diamond.ac.uk/viewer/react/preview/target/MUREECA (original fragment screen, not all structures curated)

MurE: https://fragalysis.diamond.ac.uk/viewer/react/preview/target/MUREECOLI (structures in PDB)

Other views of the targets with fragments bound can be found embedded in the wiki pages (MurD and MurE)

Other Published Xstals with Binders:

2JFF: E. coli MurD with D-Glu containing sulfonamide inhibitor

2JFH: E. coli MurD with L-Glu containing sulfonamide inhibitor

2UUO: E. coli MurD with D-Glu containing sulfonamide inhibitor LK3

2UUP: E. coli MurD with D-Glu containing sulfonamide inhibitor LK4

2VTD: E. coli MurD with D-Glu containing sulfonamide inhibitor LKM

2VTE: E. coli MurD with D-Glu containing sulfonamide inhibitor IK4

2Y67: E. coli K12 MurD with 5-Benzylidenethiazolidine-4-one Inhibitors N21

2X5O: E. coli K12 MurD with 5-Benzylidenerhodanine- and 5-Benzylidene- thiazolidine-2,4-dione Inhibitors VSV

3ZM5: Streptococcus pneumoniae R6 MurF with CYANOTHIOPHENE INHIBITOR IGM

3ZM6: Streptococcus pneumoniae R6 MurF with CYANOTHIOPHENE INHIBITOR 2GN