data_2CD5

_entry.id  2CD5
#
loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.details
1  polymer      syn  "5'-R(*GP*GP*AP*AP*GP*UP*CP*CP*GP*GP*UP*CP*UP *UP*CP*GP*GP*AP*CP*CP*GP*GP*CP*UP*UP*CP*C)-3'"  8633.143  1  ?  ?  "P4 STEM, RESIDUES 1-27"  ?  
2  non-polymer  syn  "COBALT HEXAMMINE(III)"                                                                        161.116  1  ?  ?  ?                         ?  
#
loop_
_struct_asym.id
_struct_asym.pdbx_blank_PDB_chainid_flag
_struct_asym.pdbx_modified
_struct_asym.entity_id
_struct_asym.details
A  ?     N  1  ?  
B  ?     N  2  ?  
#
_pdbx_vrpt_database.id             PDB
_pdbx_vrpt_database.code           2CD5
_pdbx_vrpt_database.extended_code  pdb_00002cd5
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   nmr
#
_pdbx_vrpt_summary.entry_id                    2CD5
_pdbx_vrpt_summary.extended_entry_id           pdb_00002cd5
_pdbx_vrpt_summary.PDB_deposition_date         2006-01-19
_pdbx_vrpt_summary.PDB_revision_number         3
_pdbx_vrpt_summary.PDB_revision_date           2024-05-15
_pdbx_vrpt_summary.RNA_suiteness               0.28
_pdbx_vrpt_summary.report_creation_date        2026-03-05:20:13
_pdbx_vrpt_summary.attempted_validation_steps  mogul,molprobity,validation-pack,coreclust,chemicalshiftanalysis,validation_schema,percentiles,writepdf,writexml,writecif
_pdbx_vrpt_summary.ligands_for_buster_report   N
#
loop_
_pdbx_vrpt_entity.id
_pdbx_vrpt_entity.type
_pdbx_vrpt_entity.description
1  polymer      "5'-R(*GP*GP*AP*AP*GP*UP*CP*CP*GP*GP*UP*CP*UP *UP*CP*GP*GP*AP*CP*CP*GP*GP*CP*UP*UP*CP*C)-3'"  
2  non-polymer  "COBALT HEXAMMINE(III)"  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all  pdb    
2  nmr  x-ray  
#
loop_
_pdbx_vrpt_percentile_type.id
_pdbx_vrpt_percentile_type.type
1  all_atom_clashscore   
2  RNAsuiteness_percent  
#
loop_
_pdbx_vrpt_percentile_conditions.id
_pdbx_vrpt_percentile_conditions.percentile_list_id
_pdbx_vrpt_percentile_conditions.type_id
_pdbx_vrpt_percentile_conditions.rank
_pdbx_vrpt_percentile_conditions.number_entries_total
_pdbx_vrpt_percentile_conditions.res_high
_pdbx_vrpt_percentile_conditions.res_low
1  1  1   5.06  229148  ?     ?     
2  2  1  24.28   14424  ?     ?     
3  1  2  18.01    8273  ?     ?     
4  2  2  40.54     777  ?     ?     
#
_pdbx_vrpt_summary_entity_geometry.ordinal          1
_pdbx_vrpt_summary_entity_geometry.PDB_model_num    1
_pdbx_vrpt_summary_entity_geometry.entity_id        1
_pdbx_vrpt_summary_entity_geometry.label_asym_id    A
_pdbx_vrpt_summary_entity_geometry.auth_asym_id     A
_pdbx_vrpt_summary_entity_geometry.angles_RMSZ      1.03
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.70
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   635
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  988
#
_pdbx_vrpt_summary_geometry.ordinal                 1
_pdbx_vrpt_summary_geometry.clashscore              28.74
_pdbx_vrpt_summary_geometry.clashscore_full_length  31.03
_pdbx_vrpt_summary_geometry.num_H_reduce            293
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ          635
_pdbx_vrpt_summary_geometry.bonds_RMSZ              0.70
_pdbx_vrpt_summary_geometry.num_angles_RMSZ         988
_pdbx_vrpt_summary_geometry.angles_RMSZ             1.03
#
loop_
_pdbx_vrpt_model_instance.id
_pdbx_vrpt_model_instance.PDB_model_num
_pdbx_vrpt_model_instance.entity_id
_pdbx_vrpt_model_instance.label_asym_id
_pdbx_vrpt_model_instance.label_seq_id
_pdbx_vrpt_model_instance.label_comp_id
_pdbx_vrpt_model_instance.auth_asym_id
_pdbx_vrpt_model_instance.auth_seq_id
_pdbx_vrpt_model_instance.label_alt_id
_pdbx_vrpt_model_instance.PDB_ins_code
_pdbx_vrpt_model_instance.count_clashes
 1  1  1  A   1  G    A     1  .  ?        3  
 2  1  1  A   2  G    A     2  .  ?        3  
 3  1  1  A   3  A    A     3  .  ?        2  
 4  1  1  A   4  A    A     4  .  ?        2  
 5  1  1  A   5  G    A     5  .  ?        1  
 6  1  1  A   6  U    A     6  .  ?        2  
 7  1  1  A   7  C    A     7  .  ?        1  
 8  1  1  A   8  C    A     8  .  ?        ?  
 9  1  1  A   9  G    A     9  .  ?        1  
10  1  1  A  10  G    A    10  .  ?        3  
11  1  1  A  11  U    A    11  .  ?        2  
12  1  1  A  12  C    A    12  .  ?        5  
13  1  1  A  13  U    A    13  .  ?        5  
14  1  1  A  14  U    A    14  .  ?        1  
15  1  1  A  15  C    A    15  .  ?        5  
16  1  1  A  16  G    A    16  .  ?        7  
17  1  1  A  17  G    A    17  .  ?        4  
18  1  1  A  18  A    A    18  .  ?        1  
19  1  1  A  19  C    A    19  .  ?        ?  
20  1  1  A  20  C    A    20  .  ?        2  
21  1  1  A  21  G    A    21  .  ?        ?  
22  1  1  A  22  G    A    22  .  ?        ?  
23  1  1  A  23  C    A    23  .  ?        ?  
24  1  1  A  24  U    A    24  .  ?        ?  
25  1  1  A  25  U    A    25  .  ?        ?  
26  1  1  A  26  C    A    26  .  ?        ?  
27  1  1  A  27  C    A    27  .  ?        ?  
28  1  2  B   .  NCO  A  1028  .  ?        ?  
#
loop_
_pdbx_vrpt_model_instance_geometry.ordinal
_pdbx_vrpt_model_instance_geometry.instance_id
_pdbx_vrpt_model_instance_geometry.RNA_score
_pdbx_vrpt_model_instance_geometry.RNA_suite
_pdbx_vrpt_model_instance_geometry.RNA_pucker
_pdbx_vrpt_model_instance_geometry.num_H_reduce
_pdbx_vrpt_model_instance_geometry.num_bonds_RMSZ
_pdbx_vrpt_model_instance_geometry.bonds_RMSZ
_pdbx_vrpt_model_instance_geometry.num_angles_RMSZ
_pdbx_vrpt_model_instance_geometry.angles_RMSZ
_pdbx_vrpt_model_instance_geometry.program_for_bond_angle_geometry
 1   1  0.00  NotAvailable       ?          12  23  0.63    37  1.15  molprobity  
 2   2  0.04  Rotameric          ?          11  26  0.62    41  1.04  molprobity  
 3   3  0.41  Rotameric          ?          11  25  0.67    39  1.01  molprobity  
 4   4  0.34  Rotameric          ?          11  25  0.69    39  1.04  molprobity  
 5   5  0.41  Rotameric          ?          11  26  0.54    41  0.75  molprobity  
 6   6  0.00  NonRotameric       outlier    10  22  0.79    34  1.09  molprobity  
 7   7  0.00  Triaged/NotBinned  ?          11  22  0.78    34  1.11  molprobity  
 8   8  0.05  Rotameric          ?          11  22  0.71    34  1.10  molprobity  
 9   9  0.33  Rotameric          ?          11  26  0.65    41  0.98  molprobity  
10  10  0.72  Rotameric          ?          11  26  0.67    41  0.98  molprobity  
11  11  0.66  Rotameric          ?          10  22  0.78    34  1.10  molprobity  
12  12  0.13  Rotameric          ?          11  22  0.78    34  1.10  molprobity  
13  13  0.14  Rotameric          ?          10  22  0.81    34  1.10  molprobity  
14  14  0.00  NonRotameric       ?          10  22  0.72    34  0.91  molprobity  
15  15  0.00  NonRotameric       ?          11  22  0.70    34  0.98  molprobity  
16  16  0.00  Triaged/NotBinned  ?          11  26  0.76    41  0.93  molprobity  
17  17  0.00  Triaged/NotBinned  ?          11  26  0.76    41  0.98  molprobity  
18  18  0.61  Rotameric          ?          11  25  0.72    39  1.02  molprobity  
19  19  0.74  Rotameric          ?          11  22  0.73    34  1.09  molprobity  
20  20  0.60  Rotameric          ?          11  22  0.72    34  1.10  molprobity  
21  21  0.14  Rotameric          ?          11  26  0.64    41  1.01  molprobity  
22  22  0.41  Rotameric          ?          11  26  0.62    41  0.99  molprobity  
23  23  0.29  Rotameric          ?          11  22  0.69    34  1.08  molprobity  
24  24  0.20  Rotameric          ?          10  22  0.76    34  1.10  molprobity  
25  25  0.40  Rotameric          ?          10  22  0.71    34  1.09  molprobity  
26  26  0.51  Rotameric          ?          11  22  0.71    34  1.13  molprobity  
27  27  0.19  Rotameric          ?          12  21  0.65    30  0.75  molprobity  
28  28     ?  ?                  ?           ?   6  0.93     ?     ?  mogul       
#
loop_
_pdbx_vrpt_instance_clashes.ordinal
_pdbx_vrpt_instance_clashes.instance_id
_pdbx_vrpt_instance_clashes.label_atom_id
_pdbx_vrpt_instance_clashes.cid
_pdbx_vrpt_instance_clashes.clashmag
_pdbx_vrpt_instance_clashes.dist
 1   1  "HO2'"   1  0.46  1.49  
 2   1  "O2'"    2  0.46  2.34  
 3   1  "O2'"    3  0.45  2.68  
 4   2  H8       1  0.46  1.49  
 5   2  "O4'"    2  0.46  2.34  
 6   2  C8       3  0.45  2.68  
 7   3  "O2'"    4  0.47  2.10  
 8   3  "H2'"    5  0.46  2.11  
 9   4  "H5'"    4  0.47  2.10  
10   4  "O4'"    5  0.46  2.11  
11   5  "O2'"    6  0.47  2.09  
12   6  "O2'"    7  0.53  2.58  
13   6  "H2'"    6  0.47  2.09  
14   7  C6       7  0.53  2.58  
15   9  "O2'"    8  0.52  2.05  
16  10  N2       9  0.53  2.76  
17  10  "H5'"    8  0.52  2.05  
18  10  C2      10  0.50  2.80  
19  11  "O2'"   11  0.63  1.94  
20  11  "C2'"   12  0.41  2.69  
21  12  "H5'"   11  0.63  1.94  
22  12  C5      13  0.55  2.94  
23  12  N3      14  0.43  2.52  
24  12  C4      15  0.42  3.07  
25  12  "O5'"   12  0.41  2.69  
26  13  C5      13  0.55  2.94  
27  13  "O2'"   16  0.51  2.64  
28  13  "O2'"   17  0.47  2.09  
29  13  "O2'"   18  0.41  1.99  
30  13  C6      15  0.42  3.07  
31  14  "H5''"  17  0.47  2.09  
32  15  "O2'"   19  0.55  2.40  
33  15  "O2'"   20  0.41  2.64  
34  15  C5      16  0.51  2.64  
35  15  "HO2'"  21  0.46  2.07  
36  15  H5      18  0.41  1.99  
37  16  "H2'"   22  0.69  1.87  
38  16  N7      23  0.55  2.55  
39  16  N2      19  0.55  2.40  
40  16  N2      21  0.46  2.07  
41  16  O6      24  0.44  2.51  
42  16  O6      14  0.43  2.52  
43  16  C2      20  0.41  2.64  
44  17  "O4'"   22  0.69  1.87  
45  17  N3      23  0.55  2.55  
46  17  "O2'"   25  0.48  2.08  
47  17  N1      24  0.44  2.51  
48  18  "H5'"   25  0.48  2.08  
49  20  C2       9  0.53  2.76  
50  20  N3      10  0.50  2.80  
#
loop_
_pdbx_vrpt_software.ordinal
_pdbx_vrpt_software.name
_pdbx_vrpt_software.version
_pdbx_vrpt_software.success_y_or_n
1  molprobity             "4-5-2 with Phenix2.0"                                              Y  
2  mogul                  "2022.3.0, CSD as543be (2022)"                                      Y  
3  buster-report          "wwPDB partial adaption of 1.1.7 (2018)"                            Y  
4  coreclust              unknown                                                             N  
5  chemicalshiftanalysis  unknown                                                             N  
6  percentiles            "20250101.v01 (using entries in the PDB archive January 1st 2025)"  N  
7  validation-pipeline    2.49                                                                Y  
##
