data_6RPU
#
_model_server_result.job_id            3_NzeE5ijdJ44hu47G6ThQ 
_model_server_result.datetime_utc      '2024-11-18 07:52:08' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          6rpu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":602}' 
#
_entry.id    6RPU 
#
_exptl.entry_id    6RPU 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            6RPU 
_cell.length_a            148.538 
_cell.length_b            148.538 
_cell.length_c            103.828 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6RPU 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        97 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 4 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4,5,6,7,8 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 
3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 
4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 
5 'crystal symmetry operation' 5_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 0 0 103.828 
6 'crystal symmetry operation' 6_556 x,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 103.828 
7 'crystal symmetry operation' 7_556 y,x,-z+1 0 1 0 1 0 0 0 0 -1 0 0 103.828 
8 'crystal symmetry operation' 8_556 -y,-x,-z+1 0 -1 0 -1 0 0 0 0 -1 0 0 103.828 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C10 H15 N5 O11 P2' 
_chem_comp.formula_weight    443.201 
_chem_comp.id                GDP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "GUANOSINE-5'-DIPHOSPHATE" 
_chem_comp.type              'rna linking' 
_chem_comp.pdbx_synonyms     ? 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
PB O1B GDP doub 181 n n 
PB O2B GDP sing 182 n n 
PB O3B GDP sing 183 n n 
PB O3A GDP sing 184 n n 
O2B HOB2 GDP sing 185 n n 
O3B HOB3 GDP sing 186 n n 
O3A PA GDP sing 187 n n 
PA O1A GDP doub 188 n n 
PA O2A GDP sing 189 n n 
PA O5' GDP sing 190 n n 
O2A HOA2 GDP sing 191 n n 
O5' C5' GDP sing 192 n n 
C5' C4' GDP sing 193 n n 
C5' H5' GDP sing 194 n n 
C5' "H5''" GDP sing 195 n n 
C4' O4' GDP sing 196 n n 
C4' C3' GDP sing 197 n n 
C4' H4' GDP sing 198 n n 
O4' C1' GDP sing 199 n n 
C3' O3' GDP sing 200 n n 
C3' C2' GDP sing 201 n n 
C3' H3' GDP sing 202 n n 
O3' HO3' GDP sing 203 n n 
C2' O2' GDP sing 204 n n 
C2' C1' GDP sing 205 n n 
C2' H2' GDP sing 206 n n 
O2' HO2' GDP sing 207 n n 
C1' N9 GDP sing 208 n n 
C1' H1' GDP sing 209 n n 
N9 C8 GDP sing 210 n y 
N9 C4 GDP sing 211 n y 
C8 N7 GDP doub 212 n y 
C8 H8 GDP sing 213 n n 
N7 C5 GDP sing 214 n y 
C5 C6 GDP sing 215 n n 
C5 C4 GDP doub 216 n y 
C6 O6 GDP doub 217 n n 
C6 N1 GDP sing 218 n n 
N1 C2 GDP sing 219 n n 
N1 HN1 GDP sing 220 n n 
C2 N2 GDP sing 221 n n 
C2 N3 GDP doub 222 n n 
N2 HN21 GDP sing 223 n n 
N2 HN22 GDP sing 224 n n 
N3 C4 GDP sing 225 n n 
#
_atom_sites.entry_id                     6RPU 
_atom_sites.fract_transf_matrix[1][1]    0.006732 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006732 
_atom_sites.fract_transf_matrix[2][3]    0 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.009631 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
B 2 G5P A 1 601 601 G5P G5P . 
C 3 GDP A 1 602 602 GDP GDP . 
D 4 ACT A 1 603 701 ACT ACT . 
E 4 ACT A 1 604 702 ACT ACT . 
F 4 ACT A 1 605 801 ACT ACT . 
G 4 ACT A 1 606 901 ACT ACT . 
H 5 HOH A 1 701 31 HOH HOH . 
H 5 HOH A 2 702 20 HOH HOH . 
H 5 HOH A 3 703 4 HOH HOH . 
H 5 HOH A 4 704 10 HOH HOH . 
H 5 HOH A 5 705 17 HOH HOH . 
H 5 HOH A 6 706 5 HOH HOH . 
H 5 HOH A 7 707 1 HOH HOH . 
H 5 HOH A 8 708 54 HOH HOH . 
H 5 HOH A 9 709 21 HOH HOH . 
H 5 HOH A 10 710 24 HOH HOH . 
H 5 HOH A 11 711 8 HOH HOH . 
H 5 HOH A 12 712 15 HOH HOH . 
H 5 HOH A 13 713 18 HOH HOH . 
H 5 HOH A 14 714 13 HOH HOH . 
H 5 HOH A 15 715 27 HOH HOH . 
H 5 HOH A 16 716 2 HOH HOH . 
H 5 HOH A 17 717 3 HOH HOH . 
H 5 HOH A 18 718 9 HOH HOH . 
H 5 HOH A 19 719 11 HOH HOH . 
H 5 HOH A 20 720 19 HOH HOH . 
H 5 HOH A 21 721 50 HOH HOH . 
H 5 HOH A 22 722 29 HOH HOH . 
H 5 HOH A 23 723 44 HOH HOH . 
H 5 HOH A 24 724 16 HOH HOH . 
H 5 HOH A 25 725 49 HOH HOH . 
H 5 HOH A 26 726 34 HOH HOH . 
H 5 HOH A 27 727 43 HOH HOH . 
H 5 HOH A 28 728 22 HOH HOH . 
H 5 HOH A 29 729 42 HOH HOH . 
H 5 HOH A 30 730 52 HOH HOH . 
H 5 HOH A 31 731 26 HOH HOH . 
H 5 HOH A 32 732 47 HOH HOH . 
H 5 HOH A 33 733 30 HOH HOH . 
H 5 HOH A 34 734 38 HOH HOH . 
H 5 HOH A 35 735 39 HOH HOH . 
H 5 HOH A 36 736 36 HOH HOH . 
H 5 HOH A 37 737 33 HOH HOH . 
H 5 HOH A 38 738 45 HOH HOH . 
H 5 HOH A 39 739 55 HOH HOH . 
H 5 HOH A 40 740 40 HOH HOH . 
H 5 HOH A 41 741 53 HOH HOH . 
H 5 HOH A 42 742 41 HOH HOH . 
H 5 HOH A 43 743 51 HOH HOH . 
H 5 HOH A 44 744 46 HOH HOH . 
H 5 HOH A 45 745 56 HOH HOH . 
H 5 HOH A 46 746 14 HOH HOH . 
H 5 HOH A 47 747 35 HOH HOH . 
H 5 HOH A 48 748 6 HOH HOH . 
H 5 HOH A 49 749 7 HOH HOH . 
H 5 HOH A 50 750 48 HOH HOH . 
H 5 HOH A 51 751 37 HOH HOH . 
H 5 HOH A 52 752 12 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 P PB GDP . . . C 3 1.584 -50.406 29.203 1 79.9 ? PB GDP 602 A 1 
HETATM 2 O O1B GDP . . . C 3 0.954 -49.589 28.109 1 81.35 ? O1B GDP 602 A 1 
HETATM 3 O O2B GDP . . . C 3 1.106 -50.079 30.594 1 78.58 ? O2B GDP 602 A 1 
HETATM 4 O O3B GDP . . . C 3 3.074 -50.565 29.083 1 80.63 ? O3B GDP 602 A 1 
HETATM 5 O O3A GDP . . . C 3 1.036 -51.877 28.9 1 82.28 ? O3A GDP 602 A 1 
HETATM 6 P PA GDP . . . C 3 -0.415 -52.385 29.358 1 84.35 ? PA GDP 602 A 1 
HETATM 7 O O1A GDP . . . C 3 -1.395 -52.153 28.241 1 82.13 ? O1A GDP 602 A 1 
HETATM 8 O O2A GDP . . . C 3 -0.709 -51.867 30.738 1 82.71 ? O2A GDP 602 A 1 
HETATM 9 O O5' GDP . . . C 3 -0.1 -53.957 29.436 1 81.35 ? O5' GDP 602 A 1 
HETATM 10 C C5' GDP . . . C 3 -0.591 -54.778 30.487 1 83.05 ? C5' GDP 602 A 1 
HETATM 11 C C4' GDP . . . C 3 0.379 -55.936 30.683 1 82.09 ? C4' GDP 602 A 1 
HETATM 12 O O4' GDP . . . C 3 1.712 -55.43 30.745 1 81.21 ? O4' GDP 602 A 1 
HETATM 13 C C3' GDP . . . C 3 0.098 -56.69 31.974 1 82.3 ? C3' GDP 602 A 1 
HETATM 14 O O3' GDP . . . C 3 -0.284 -58.04 31.678 1 83.57 ? O3' GDP 602 A 1 
HETATM 15 C C2' GDP . . . C 3 1.377 -56.606 32.793 1 81.51 ? C2' GDP 602 A 1 
HETATM 16 O O2' GDP . . . C 3 1.866 -57.894 33.194 1 81.08 ? O2' GDP 602 A 1 
HETATM 17 C C1' GDP . . . C 3 2.393 -55.904 31.904 1 76.71 ? C1' GDP 602 A 1 
HETATM 18 N N9 GDP . . . C 3 3.003 -54.749 32.601 1 68.11 ? N9 GDP 602 A 1 
HETATM 19 C C8 GDP . . . C 3 2.795 -53.461 32.282 1 71.75 ? C8 GDP 602 A 1 
HETATM 20 N N7 GDP . . . C 3 3.498 -52.647 33.106 1 71.67 ? N7 GDP 602 A 1 
HETATM 21 C C5 GDP . . . C 3 4.173 -53.422 33.969 1 73.59 ? C5 GDP 602 A 1 
HETATM 22 C C6 GDP . . . C 3 5.103 -53.2 35.094 1 68.45 ? C6 GDP 602 A 1 
HETATM 23 O O6 GDP . . . C 3 5.425 -52.043 35.432 1 67.9 ? O6 GDP 602 A 1 
HETATM 24 N N1 GDP . . . C 3 5.586 -54.27 35.734 1 69.91 ? N1 GDP 602 A 1 
HETATM 25 C C2 GDP . . . C 3 5.247 -55.522 35.381 1 72.15 ? C2 GDP 602 A 1 
HETATM 26 N N2 GDP . . . C 3 5.775 -56.557 36.077 1 73.35 ? N2 GDP 602 A 1 
HETATM 27 N N3 GDP . . . C 3 4.401 -55.799 34.36 1 73.14 ? N3 GDP 602 A 1 
HETATM 28 C C4 GDP . . . C 3 3.846 -54.808 33.631 1 72.02 ? C4 GDP 602 A 1 
HETATM 29 H H5' GDP . . . C 3 -1.581 -55.161 30.23 1 101.31 ? H5' GDP 602 A 1 
HETATM 30 H "H5''" GDP . . . C 3 -0.673 -54.199 31.409 1 101.31 ? "H5''" GDP 602 A 1 
HETATM 31 H H4' GDP . . . C 3 0.28 -56.63 29.837 1 100.16 ? H4' GDP 602 A 1 
HETATM 32 H H3' GDP . . . C 3 -0.709 -56.178 32.516 1 100.41 ? H3' GDP 602 A 1 
HETATM 33 H HO3' GDP . . . C 3 -0.504 -58.5 32.499 1 101.93 ? HO3' GDP 602 A 1 
HETATM 34 H H2' GDP . . . C 3 1.19 -55.983 33.68 1 99.46 ? H2' GDP 602 A 1 
HETATM 35 H HO2' GDP . . . C 3 1.191 -58.348 33.716 1 98.95 ? HO2' GDP 602 A 1 
HETATM 36 H H1' GDP . . . C 3 3.172 -56.624 31.616 1 93.7 ? H1' GDP 602 A 1 
HETATM 37 H H8 GDP . . . C 3 2.152 -53.12 31.48 1 87.74 ? H8 GDP 602 A 1 
HETATM 38 H HN1 GDP . . . C 3 6.24 -54.129 36.53 1 85.54 ? HN1 GDP 602 A 1 
HETATM 39 H HN21 GDP . . . C 3 6.409 -56.379 36.843 1 89.67 ? HN21 GDP 602 A 1 
HETATM 40 H HN22 GDP . . . C 3 5.536 -57.506 35.829 1 89.67 ? HN22 GDP 602 A 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           41 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           238 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           40 
#