Ligand validation:2PMD

GDP: GUANOSINE-5'-DIPHOSPHATE

GDP is a Ligand Of Interest in 2PMD designated by the RCSB

	Best-fitted instance in this entry
	Other instances in this entry

	Best-fitted instance in this entry
	Best-fitted PDB instances with same target (top 5)

	Best-fitted instance in this entry
	Best-fitted PDB instances with different target (top 5)

Identifier	Ranking for goodness of fit	Ranking for geometry	Real space R factor	Real space correlation coefficient	RMSZ-bond-length	RMSZ-bond-angle	Outliers of bond length	Outliers of bond angle	Atomic clashes	Stereochemical errors	Model completeness	Average occupancy
2PMD_GDP_A_416	18%	23%	0.23	0.819	1.31	1.87	2	6	6	0	100%	1
2PMD_GDP_B_416	12%	24%	0.252	0.782	1.24	1.85	2	6	2	0	100%	1
4RD0_GDP_A_501	97%	47%	0.065	0.981	0.86	1.18	-	4	0	0	100%	1
4RD1_GDP_A_502	95%	45%	0.075	0.978	0.92	1.2	1	3	0	0	100%	17
6I5M_GDP_A_501	95%	46%	0.088	0.991	0.79	1.28	1	4	0	0	100%	1
4RD3_GDP_A_502	92%	45%	0.084	0.975	0.88	1.24	1	5	0	0	100%	1
4M4S_GDP_A_530	91%	46%	0.099	0.985	0.97	1.12	1	2	2	0	100%	0.9557
1RRG_GDP_A_183	100%	17%	0.036	0.997	2.05	1.56	7	3	0	0	100%	1
2CXX_GDP_B_2401	100%	29%	0.031	0.989	1.26	1.57	1	3	0	0	100%	1
4LUC_GDP_A_204	100%	40%	0.036	0.992	1.22	1.11	2	2	0	0	100%	1
5YMX_GDP_A_301	100%	54%	0.038	0.994	0.92	0.85	1	-	2	0	100%	1
5KY2_GDP_A_403	100%	48%	0.036	0.989	0.98	1.04	1	1	0	0	100%	1

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.