data_2H7V
#
_model_server_result.job_id            EsfRGEG5EkQsjR6xYA_l6w 
_model_server_result.datetime_utc      '2025-07-17 13:58:17' 
_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          2h7v 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":200}' 
#
_entry.id    2H7V 
#
_exptl.entry_id    2H7V 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         92.08 
_cell.angle_beta          103.38 
_cell.angle_gamma         115.79 
_cell.entry_id            2H7V 
_cell.length_a            66.398 
_cell.length_b            75.519 
_cell.length_c            99.772 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2H7V 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 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
? dimeric 2 author_defined_assembly 1 
? dimeric 2 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E,F,I,K 1 1 
B,D,G,H,J,L 2 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 F N N 
? 4 H 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 A OG1 THR 21 A THR 17 1_555 E MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? 
metalc ? metalc2 A O THR 39 A THR 35 1_555 E MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? 
metalc ? metalc3 F O1B GDP . A GDP 200 1_555 E MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.957 ? 
metalc ? metalc4 F O3B GDP . A GDP 200 1_555 E MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? 
metalc ? metalc5 B OG1 THR 21 B THR 17 1_555 G MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? 
metalc ? metalc6 B O THR 39 B THR 35 1_555 G MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? 
metalc ? metalc7 H O3B GDP . B GDP 200 1_555 G MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? 
metalc ? metalc8 H O1B GDP . B GDP 200 1_555 G MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.136 ? 
#
_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                     2H7V 
_atom_sites.fract_transf_matrix[1][1]    0.015061 
_atom_sites.fract_transf_matrix[1][2]    0.007277 
_atom_sites.fract_transf_matrix[1][3]    0.004779 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014707 
_atom_sites.fract_transf_matrix[2][3]    0.002328 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.010431 
_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
E 3 MG A 1 201 201 MG MG . 
F 4 GDP A 1 200 200 GDP GDP . 
G 3 MG B 1 201 201 MG MG . 
H 4 GDP B 1 200 200 GDP GDP . 
I 5 HOH A 1 202 22 HOH HOH . 
I 5 HOH A 2 203 25 HOH HOH . 
I 5 HOH A 3 204 41 HOH HOH . 
I 5 HOH A 4 205 43 HOH HOH . 
I 5 HOH A 5 206 45 HOH HOH . 
I 5 HOH A 6 207 50 HOH HOH . 
I 5 HOH A 7 208 59 HOH HOH . 
I 5 HOH A 8 209 64 HOH HOH . 
I 5 HOH A 9 210 76 HOH HOH . 
J 5 HOH B 1 202 15 HOH HOH . 
J 5 HOH B 2 203 17 HOH HOH . 
J 5 HOH B 3 204 26 HOH HOH . 
J 5 HOH B 4 205 33 HOH HOH . 
J 5 HOH B 5 206 38 HOH HOH . 
J 5 HOH B 6 207 44 HOH HOH . 
J 5 HOH B 7 208 58 HOH HOH . 
J 5 HOH B 8 209 67 HOH HOH . 
J 5 HOH B 9 210 70 HOH HOH . 
J 5 HOH B 10 211 74 HOH HOH . 
K 5 HOH C 1 1 1 HOH HOH . 
K 5 HOH C 2 3 3 HOH HOH . 
K 5 HOH C 3 4 4 HOH HOH . 
K 5 HOH C 4 5 5 HOH HOH . 
K 5 HOH C 5 7 7 HOH HOH . 
K 5 HOH C 6 8 8 HOH HOH . 
K 5 HOH C 7 9 9 HOH HOH . 
K 5 HOH C 8 10 10 HOH HOH . 
K 5 HOH C 9 13 13 HOH HOH . 
K 5 HOH C 10 16 16 HOH HOH . 
K 5 HOH C 11 20 20 HOH HOH . 
K 5 HOH C 12 21 21 HOH HOH . 
K 5 HOH C 13 27 27 HOH HOH . 
K 5 HOH C 14 28 28 HOH HOH . 
K 5 HOH C 15 29 29 HOH HOH . 
K 5 HOH C 16 30 30 HOH HOH . 
K 5 HOH C 17 35 35 HOH HOH . 
K 5 HOH C 18 40 40 HOH HOH . 
K 5 HOH C 19 47 47 HOH HOH . 
K 5 HOH C 20 48 48 HOH HOH . 
K 5 HOH C 21 49 49 HOH HOH . 
K 5 HOH C 22 52 52 HOH HOH . 
K 5 HOH C 23 53 53 HOH HOH . 
K 5 HOH C 24 56 56 HOH HOH . 
K 5 HOH C 25 57 57 HOH HOH . 
K 5 HOH C 26 62 62 HOH HOH . 
K 5 HOH C 27 63 63 HOH HOH . 
K 5 HOH C 28 65 65 HOH HOH . 
K 5 HOH C 29 68 68 HOH HOH . 
K 5 HOH C 30 69 69 HOH HOH . 
K 5 HOH C 31 75 75 HOH HOH . 
K 5 HOH C 32 78 78 HOH HOH . 
L 5 HOH D 1 2 2 HOH HOH . 
L 5 HOH D 2 6 6 HOH HOH . 
L 5 HOH D 3 11 11 HOH HOH . 
L 5 HOH D 4 12 12 HOH HOH . 
L 5 HOH D 5 14 14 HOH HOH . 
L 5 HOH D 6 18 18 HOH HOH . 
L 5 HOH D 7 19 19 HOH HOH . 
L 5 HOH D 8 23 23 HOH HOH . 
L 5 HOH D 9 24 24 HOH HOH . 
L 5 HOH D 10 31 31 HOH HOH . 
L 5 HOH D 11 32 32 HOH HOH . 
L 5 HOH D 12 34 34 HOH HOH . 
L 5 HOH D 13 36 36 HOH HOH . 
L 5 HOH D 14 37 37 HOH HOH . 
L 5 HOH D 15 39 39 HOH HOH . 
L 5 HOH D 16 42 42 HOH HOH . 
L 5 HOH D 17 46 46 HOH HOH . 
L 5 HOH D 18 51 51 HOH HOH . 
L 5 HOH D 19 54 54 HOH HOH . 
L 5 HOH D 20 55 55 HOH HOH . 
L 5 HOH D 21 60 60 HOH HOH . 
L 5 HOH D 22 66 66 HOH HOH . 
L 5 HOH D 23 71 71 HOH HOH . 
L 5 HOH D 24 72 72 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 . . . H 4 -9.627 -9.257 -89.744 1 59.63 ? PB GDP 200 B 1 
HETATM 2 O O1B GDP . . . H 4 -9.599 -10.04 -88.457 1 59.99 ? O1B GDP 200 B 1 
HETATM 3 O O2B GDP . . . H 4 -9.03 -10.109 -90.805 1 58.46 ? O2B GDP 200 B 1 
HETATM 4 O O3B GDP . . . H 4 -11.089 -8.864 -89.891 1 60.91 ? O3B GDP 200 B 1 
HETATM 5 O O3A GDP . . . H 4 -8.732 -7.93 -89.754 1 62.55 ? O3A GDP 200 B 1 
HETATM 6 P PA GDP . . . H 4 -9.39 -6.449 -89.823 1 65.46 ? PA GDP 200 B 1 
HETATM 7 O O1A GDP . . . H 4 -10.014 -6.087 -91.129 1 65.34 ? O1A GDP 200 B 1 
HETATM 8 O O2A GDP . . . H 4 -10.36 -6.145 -88.702 1 63.34 ? O2A GDP 200 B 1 
HETATM 9 O O5' GDP . . . H 4 -8.035 -5.613 -89.883 1 71.08 ? O5' GDP 200 B 1 
HETATM 10 C C5' GDP . . . H 4 -7.023 -5.6 -88.881 1 73.49 ? C5' GDP 200 B 1 
HETATM 11 C C4' GDP . . . H 4 -6.434 -4.224 -89.06 1 76.6 ? C4' GDP 200 B 1 
HETATM 12 O O4' GDP . . . H 4 -5.683 -4.218 -90.279 1 77.22 ? O4' GDP 200 B 1 
HETATM 13 C C3' GDP . . . H 4 -7.543 -3.18 -89.215 1 78.57 ? C3' GDP 200 B 1 
HETATM 14 O O3' GDP . . . H 4 -7.843 -2.516 -87.987 1 79.26 ? O3' GDP 200 B 1 
HETATM 15 C C2' GDP . . . H 4 -7.024 -2.242 -90.273 1 79.34 ? C2' GDP 200 B 1 
HETATM 16 O O2' GDP . . . H 4 -6.52 -1.044 -89.684 1 82.23 ? O2' GDP 200 B 1 
HETATM 17 C C1' GDP . . . H 4 -5.862 -2.96 -90.92 1 79.2 ? C1' GDP 200 B 1 
HETATM 18 N N9 GDP . . . H 4 -6.083 -3.114 -92.372 1 79.54 ? N9 GDP 200 B 1 
HETATM 19 C C8 GDP . . . H 4 -7.077 -3.721 -93.055 1 79.78 ? C8 GDP 200 B 1 
HETATM 20 N N7 GDP . . . H 4 -6.862 -3.603 -94.404 1 79.3 ? N7 GDP 200 B 1 
HETATM 21 C C5 GDP . . . H 4 -5.71 -2.929 -94.575 1 79.02 ? C5 GDP 200 B 1 
HETATM 22 C C6 GDP . . . H 4 -4.862 -2.44 -95.688 1 79.15 ? C6 GDP 200 B 1 
HETATM 23 O O6 GDP . . . H 4 -5.155 -2.638 -96.876 1 79.39 ? O6 GDP 200 B 1 
HETATM 24 N N1 GDP . . . H 4 -3.744 -1.76 -95.395 1 80.04 ? N1 GDP 200 B 1 
HETATM 25 C C2 GDP . . . H 4 -3.358 -1.511 -94.121 1 79.97 ? C2 GDP 200 B 1 
HETATM 26 N N2 GDP . . . H 4 -2.213 -0.827 -93.865 1 79.67 ? N2 GDP 200 B 1 
HETATM 27 N N3 GDP . . . H 4 -4.089 -1.921 -93.06 1 79.62 ? N3 GDP 200 B 1 
HETATM 28 C C4 GDP . . . H 4 -5.23 -2.611 -93.231 1 79.25 ? C4 GDP 200 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           307 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           28 
#