data_7DN9
#
_model_server_result.job_id            eVXPRZAk6dZnqMN5OgcJmA 
_model_server_result.datetime_utc      '2024-11-29 09:10:50' 
_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          7dn9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":202}' 
#
_entry.id    7DN9 
#
_exptl.entry_id    7DN9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          104.8 
_cell.angle_gamma         90 
_cell.entry_id            7DN9 
_cell.length_a            104.711 
_cell.length_b            105.576 
_cell.length_c            105.839 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7DN9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
PISA dimeric 2 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,I,J,K 1 1 
C,D,L,M,N 2 1 
E,F,O,P,Q 3 1 
G,H,R,S,T 4 1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    x,y,z 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 5 K N N 
? 5 N N N 
? 5 Q N N 
? 5 T N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc ? metalc1 B OG1 THR 32 B THR 48 1_555 J MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.86 ? 
metalc ? metalc2 J MG MG . B MG 201 1_555 K O1B GDP . B GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? 
metalc ? metalc3 M MG MG . D MG 201 1_555 N O1B GDP . D GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? 
metalc ? metalc4 F OG1 THR 32 F THR 48 1_555 P MG MG . F MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.96 ? 
metalc ? metalc5 P MG MG . F MG 201 1_555 Q O1B GDP . F GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? 
metalc ? metalc6 H OG1 THR 32 H THR 48 1_555 S MG MG . H MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.728 ? 
metalc ? metalc7 S MG MG . H MG 201 1_555 T O3B GDP . H GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? 
metalc ? metalc8 S MG MG . H MG 201 1_555 T O1B GDP . H GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? 
#
_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 83 n n 
PB O2B GDP sing 84 n n 
PB O3B GDP sing 85 n n 
PB O3A GDP sing 86 n n 
O2B HOB2 GDP sing 87 n n 
O3B HOB3 GDP sing 88 n n 
O3A PA GDP sing 89 n n 
PA O1A GDP doub 90 n n 
PA O2A GDP sing 91 n n 
PA O5' GDP sing 92 n n 
O2A HOA2 GDP sing 93 n n 
O5' C5' GDP sing 94 n n 
C5' C4' GDP sing 95 n n 
C5' H5' GDP sing 96 n n 
C5' "H5''" GDP sing 97 n n 
C4' O4' GDP sing 98 n n 
C4' C3' GDP sing 99 n n 
C4' H4' GDP sing 100 n n 
O4' C1' GDP sing 101 n n 
C3' O3' GDP sing 102 n n 
C3' C2' GDP sing 103 n n 
C3' H3' GDP sing 104 n n 
O3' HO3' GDP sing 105 n n 
C2' O2' GDP sing 106 n n 
C2' C1' GDP sing 107 n n 
C2' H2' GDP sing 108 n n 
O2' HO2' GDP sing 109 n n 
C1' N9 GDP sing 110 n n 
C1' H1' GDP sing 111 n n 
N9 C8 GDP sing 112 n y 
N9 C4 GDP sing 113 n y 
C8 N7 GDP doub 114 n y 
C8 H8 GDP sing 115 n n 
N7 C5 GDP sing 116 n y 
C5 C6 GDP sing 117 n n 
C5 C4 GDP doub 118 n y 
C6 O6 GDP doub 119 n n 
C6 N1 GDP sing 120 n n 
N1 C2 GDP sing 121 n n 
N1 HN1 GDP sing 122 n n 
C2 N2 GDP sing 123 n n 
C2 N3 GDP doub 124 n n 
N2 HN21 GDP sing 125 n n 
N2 HN22 GDP sing 126 n n 
N3 C4 GDP sing 127 n n 
#
_atom_sites.entry_id                     7DN9 
_atom_sites.fract_transf_matrix[1][1]    0.00955 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002524 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009472 
_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]    0.009773 
_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
I 3 NAD A 1 401 401 NAD NAD . 
J 4 MG B 1 201 201 MG MG . 
K 5 GDP B 1 202 202 GDP GDP . 
L 3 NAD C 1 401 401 NAD NAD . 
M 4 MG D 1 201 201 MG MG . 
N 5 GDP D 1 202 202 GDP GDP . 
O 3 NAD E 1 401 401 NAD NAD . 
P 4 MG F 1 201 201 MG MG . 
Q 5 GDP F 1 202 202 GDP GDP . 
R 3 NAD G 1 401 401 NAD NAD . 
S 4 MG H 1 201 201 MG MG . 
T 5 GDP H 1 202 202 GDP GDP . 
#
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 . . . N 5 18.726 -5.388 -39.013 1 36.81 ? PB GDP 202 D 1 
HETATM 2 O O1B GDP . . . N 5 19.461 -4.072 -38.952 1 48.03 ? O1B GDP 202 D 1 
HETATM 3 O O2B GDP . . . N 5 19.51 -6.428 -38.25 1 39.81 ? O2B GDP 202 D 1 
HETATM 4 O O3B GDP . . . N 5 17.358 -5.223 -38.397 1 37.15 ? O3B GDP 202 D 1 
HETATM 5 O O3A GDP . . . N 5 18.571 -5.857 -40.547 1 43.09 ? O3A GDP 202 D 1 
HETATM 6 P PA GDP . . . N 5 17.655 -5.023 -41.575 1 38.59 ? PA GDP 202 D 1 
HETATM 7 O O1A GDP . . . N 5 16.212 -5.448 -41.455 1 37.19 ? O1A GDP 202 D 1 
HETATM 8 O O2A GDP . . . N 5 17.799 -3.537 -41.345 1 49.81 ? O2A GDP 202 D 1 
HETATM 9 O O5' GDP . . . N 5 18.232 -5.417 -43.024 1 40.46 ? O5' GDP 202 D 1 
HETATM 10 C C5' GDP . . . N 5 18.7 -4.385 -43.888 1 46.25 ? C5' GDP 202 D 1 
HETATM 11 C C4' GDP . . . N 5 18.715 -4.867 -45.332 1 41.38 ? C4' GDP 202 D 1 
HETATM 12 O O4' GDP . . . N 5 18.816 -6.291 -45.382 1 44.72 ? O4' GDP 202 D 1 
HETATM 13 C C3' GDP . . . N 5 17.445 -4.479 -46.071 1 44.02 ? C3' GDP 202 D 1 
HETATM 14 O O3' GDP . . . N 5 17.748 -3.49 -47.058 1 55.76 ? O3' GDP 202 D 1 
HETATM 15 C C2' GDP . . . N 5 16.961 -5.743 -46.75 1 47.92 ? C2' GDP 202 D 1 
HETATM 16 O O2' GDP . . . N 5 16.834 -5.524 -48.159 1 54.99 ? O2' GDP 202 D 1 
HETATM 17 C C1' GDP . . . N 5 18.036 -6.78 -46.476 1 49.08 ? C1' GDP 202 D 1 
HETATM 18 N N9 GDP . . . N 5 17.42 -8.09 -46.152 1 45.03 ? N9 GDP 202 D 1 
HETATM 19 C C8 GDP . . . N 5 16.842 -8.429 -44.985 1 44.95 ? C8 GDP 202 D 1 
HETATM 20 N N7 GDP . . . N 5 16.38 -9.706 -45.024 1 41.97 ? N7 GDP 202 D 1 
HETATM 21 C C5 GDP . . . N 5 16.666 -10.201 -46.242 1 38.71 ? C5 GDP 202 D 1 
HETATM 22 C C6 GDP . . . N 5 16.459 -11.486 -46.948 1 40.96 ? C6 GDP 202 D 1 
HETATM 23 O O6 GDP . . . N 5 15.885 -12.442 -46.384 1 42.9 ? O6 GDP 202 D 1 
HETATM 24 N N1 GDP . . . N 5 16.907 -11.589 -48.205 1 44.5 ? N1 GDP 202 D 1 
HETATM 25 C C2 GDP . . . N 5 17.53 -10.575 -48.836 1 40.58 ? C2 GDP 202 D 1 
HETATM 26 N N2 GDP . . . N 5 17.952 -10.762 -50.11 1 38.97 ? N2 GDP 202 D 1 
HETATM 27 N N3 GDP . . . N 5 17.754 -9.371 -48.25 1 35.94 ? N3 GDP 202 D 1 
HETATM 28 C C4 GDP . . . N 5 17.351 -9.132 -46.981 1 39.06 ? C4 GDP 202 D 1 
#
_model_server_stats.io_time_ms              70 
_model_server_stats.parse_time_ms           27 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           288 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#