data_7W5R
#
_model_server_result.job_id            3YQMRWYpNBC00-WRjMp32g 
_model_server_result.datetime_utc      '2025-07-31 07:29:42' 
_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          7w5r 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"R","auth_seq_id":1002}' 
#
_entry.id    7W5R 
#
_exptl.entry_id    7W5R 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         119.986 
_cell.angle_beta          90.061 
_cell.angle_gamma         90.015 
_cell.entry_id            7W5R 
_cell.length_a            40.556 
_cell.length_b            82.513 
_cell.length_c            82.573 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7W5R 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    'P 1' 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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
? 4 J N N 
? 4 L N N 
? 4 N N N 
? 4 P N N 
? 4 R N N 
? 4 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
covale ? covale1 B NZ LYS 117 E LYS 117 1_555 L O3' GDP . E GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.296 ? 
covale ? covale2 D N SER 17 I SER 17 1_555 N O1B GDP . I GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? 
covale ? covale3 F NZ LYS 117 Q LYS 117 1_555 R O3' GDP . Q GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.297 ? 
metalc ? metalc1 I MG MG . A MG 1001 1_555 J O1B GDP . A GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? 
metalc ? metalc2 I MG MG . A MG 1001 1_555 J O2B GDP . A GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? 
metalc ? metalc3 I MG MG . A MG 1001 1_555 J O3A GDP . A GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.572 ? 
metalc ? metalc4 B OG SER 17 E SER 17 1_555 K MG MG . E MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
metalc ? metalc5 K MG MG . E MG 1001 1_555 L O3B GDP . E GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? 
metalc ? metalc6 K MG MG . E MG 1001 1_555 L O2B GDP . E GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? 
metalc ? metalc7 D OG SER 17 I SER 17 1_555 M MG MG . I MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? 
metalc ? metalc8 M MG MG . I MG 1001 1_555 N O2B GDP . I GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? 
metalc ? metalc9 E OG SER 17 M SER 17 1_555 O MG MG . M MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? 
metalc ? metalc10 E OD1 ASP 57 M ASP 57 1_555 O MG MG . M MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? 
metalc ? metalc11 E OD2 ASP 57 M ASP 57 1_555 O MG MG . M MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? 
metalc ? metalc12 O MG MG . M MG 1001 1_555 P O3B GDP . M GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.827 ? 
metalc ? metalc13 F OG SER 17 Q SER 17 1_555 Q MG MG . Q MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? 
metalc ? metalc14 Q MG MG . Q MG 1001 1_555 R O2B GDP . Q GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? 
metalc ? metalc15 G OG SER 17 U SER 17 1_555 S MG MG . U MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? 
metalc ? metalc16 S MG MG . U MG 1001 1_555 T O2B GDP . U GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
#
_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                     7W5R 
_atom_sites.fract_transf_matrix[1][1]    0.024657 
_atom_sites.fract_transf_matrix[1][2]    0.000006 
_atom_sites.fract_transf_matrix[1][3]    0.000034 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012119 
_atom_sites.fract_transf_matrix[2][3]    0.006993 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.013982 
_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 MG A 1 1001 1001 MG MG . 
J 4 GDP A 1 1002 1002 GDP GDP . 
K 3 MG E 1 1001 1001 MG MG . 
L 4 GDP E 1 1002 1002 GDP GDP . 
M 3 MG I 1 1001 1001 MG MG . 
N 4 GDP I 1 1002 1002 GDP GDP . 
O 3 MG M 1 1001 1001 MG MG . 
P 4 GDP M 1 1002 1002 GDP GDP . 
Q 3 MG Q 1 1001 1001 MG MG . 
R 4 GDP Q 1 1002 1002 GDP GDP . 
S 3 MG U 1 1001 1001 MG MG . 
T 4 GDP U 1 1002 1002 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 . . . R 4 28.341 -23.834 40.824 1 76.19 ? PB GDP 1002 Q 1 
HETATM 2 O O1B GDP . . . R 4 28.272 -23.723 39.318 1 77.77 ? O1B GDP 1002 Q 1 
HETATM 3 O O2B GDP . . . R 4 29.44 -24.795 41.21 1 70.82 ? O2B GDP 1002 Q 1 
HETATM 4 O O3B GDP . . . R 4 27.016 -24.345 41.334 1 74.45 ? O3B GDP 1002 Q 1 
HETATM 5 O O3A GDP . . . R 4 28.624 -22.382 41.465 1 76.69 ? O3A GDP 1002 Q 1 
HETATM 6 P PA GDP . . . R 4 27.35 -21.514 41.93 1 82.84 ? PA GDP 1002 Q 1 
HETATM 7 O O1A GDP . . . R 4 26.314 -21.468 40.836 1 86.1 ? O1A GDP 1002 Q 1 
HETATM 8 O O2A GDP . . . R 4 26.767 -22.095 43.197 1 82.11 ? O2A GDP 1002 Q 1 
HETATM 9 O O5' GDP . . . R 4 27.855 -20.008 42.167 1 90.29 ? O5' GDP 1002 Q 1 
HETATM 10 C C5' GDP . . . R 4 27.141 -18.999 41.458 1 98.53 ? C5' GDP 1002 Q 1 
HETATM 11 C C4' GDP . . . R 4 26.253 -18.193 42.397 1 108.79 ? C4' GDP 1002 Q 1 
HETATM 12 O O4' GDP . . . R 4 26.917 -16.989 42.782 1 122.24 ? O4' GDP 1002 Q 1 
HETATM 13 C C3' GDP . . . R 4 24.959 -17.789 41.715 1 107.21 ? C3' GDP 1002 Q 1 
HETATM 14 O O3' GDP . . . R 4 23.87 -18.46 42.352 1 92.43 ? O3' GDP 1002 Q 1 
HETATM 15 C C2' GDP . . . R 4 24.832 -16.286 41.896 1 122.49 ? C2' GDP 1002 Q 1 
HETATM 16 O O2' GDP . . . R 4 23.641 -15.978 42.627 1 122.95 ? O2' GDP 1002 Q 1 
HETATM 17 C C1' GDP . . . R 4 26.06 -15.847 42.679 1 132.1 ? C1' GDP 1002 Q 1 
HETATM 18 N N9 GDP . . . R 4 26.79 -14.783 41.945 1 149.02 ? N9 GDP 1002 Q 1 
HETATM 19 C C8 GDP . . . R 4 26.514 -14.351 40.701 1 159.13 ? C8 GDP 1002 Q 1 
HETATM 20 N N7 GDP . . . R 4 27.385 -13.38 40.316 1 164.58 ? N7 GDP 1002 Q 1 
HETATM 21 C C5 GDP . . . R 4 28.26 -13.184 41.321 1 165.19 ? C5 GDP 1002 Q 1 
HETATM 22 C C6 GDP . . . R 4 29.44 -12.312 41.58 1 174.17 ? C6 GDP 1002 Q 1 
HETATM 23 O O6 GDP . . . R 4 29.852 -11.486 40.732 1 178.7 ? O6 GDP 1002 Q 1 
HETATM 24 N N1 GDP . . . R 4 30.06 -12.434 42.761 1 174.39 ? N1 GDP 1002 Q 1 
HETATM 25 C C2 GDP . . . R 4 29.652 -13.308 43.701 1 171.57 ? C2 GDP 1002 Q 1 
HETATM 26 N N2 GDP . . . R 4 30.33 -13.375 44.873 1 174.6 ? N2 GDP 1002 Q 1 
HETATM 27 N N3 GDP . . . R 4 28.586 -14.129 43.528 1 164.83 ? N3 GDP 1002 Q 1 
HETATM 28 C C4 GDP . . . R 4 27.863 -14.119 42.387 1 158.85 ? C4 GDP 1002 Q 1 
#
_model_server_stats.io_time_ms              145 
_model_server_stats.parse_time_ms           31 
_model_server_stats.create_model_time_ms    90 
_model_server_stats.query_time_ms           301 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           28 
#