Table 1. Analysis of All Deposited GR Cocrystal Structures from the RCSB PDBa.
PDB | species | ligand | monomer A | monomer B | monomer C | monomer D |
---|---|---|---|---|---|---|
1B74 | A. pyrophilus | d-glutamine | 1 | |||
1ZUW | B. subtilis | d-glutamate | 1 | 1 | 1 | |
2DWU | B. anthracis 1 | d-glutamate | 1 | 2 | 2 | |
2GZM | B. anthracis 2 | d-glutamate | 0 | 1 | 0 | 1 |
2JFN | E. coli | d-glutamate | 1 | |||
2JFO | E. faecalis | d-glutamate | 0 | 1 | ||
2JFP | E. faecalis | d-glutamate | 1 | 1 | ||
2JFQ | S. aureus | d-glutamate | 1 | 2 | ||
2JFU | E. faecium | phosphate ions | 2 | |||
2JFV | E. faecium | citrate | 2 | |||
2JFW | E. faecium | tartaric acid | 4 | |||
2JFX | H. pylori | d-glutamate | 1 | 1 | ||
2JFY | H. pylori | d-glutamate | 1 | 2 | ||
2JFZ | H. pylori | d-glutamate | 2 | 1 | ||
2OHO | S. pyogenes | sulfate ion | 0 | 3 | ||
2OHV | S. pyogenes | naphthylmethyl-d-glu | 1 | |||
2VVT | E. faecalis | d-glutamate | 1 | 1 | ||
2W4I | H. pylori | d-glutamate | 2 | 1 | 2 | 1 |
3IST | L. monocyto. | succinic acid | 2 | 2 | ||
3ISV | L. monocyto. | acetate ion | 0 | |||
3OUT | F. tularensis | d-glutamate | 2 | 2 | 2 | |
3UHF | C. jejuni | d-glutamate | 1 | 1 | ||
3UHO | C. jejuni | d-glutamate | 1 | 1 | ||
4B1F | H. pylori | d-glutamate | 2 | 2 |
The number of interstitial waters is indicated per monomer for each structure. Structures were downloaded directly from the RCSB PDB, and hydrogen atoms were added using the “Clean All” function of YASARA v9.11.9. All non-hydrogen atoms were fixed, and an energy minimization was performed to relax hydrogen atoms. Interstitial waters are defined as a single water molecule forming at least two hydrogen bonds: one with the bound ligand and one with the enzyme. Monomer labeling is arbitrary and does not correspond to PDB labeling. Several deposited structures are unliganded and have been excluded from this analysis. Their PDB ID numbers correspond to 1B73, 3HFR, and 3UHP.