data_2H7V
#
_model_server_result.job_id            wExR8f7rto8YeQKj9Ok3wg 
_model_server_result.datetime_utc      '2024-12-19 12:29:33' 
_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":"F","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 . . . F 4 5.431 -16.023 -43.451 1 52.59 ? PB GDP 200 A 1 
HETATM 2 O O1B GDP . . . F 4 4.71 -16.677 -44.595 1 50.78 ? O1B GDP 200 A 1 
HETATM 3 O O2B GDP . . . F 4 4.286 -15.366 -42.754 1 54.41 ? O2B GDP 200 A 1 
HETATM 4 O O3B GDP . . . F 4 6.124 -16.924 -42.457 1 52.51 ? O3B GDP 200 A 1 
HETATM 5 O O3A GDP . . . F 4 6.501 -14.953 -43.967 1 54.36 ? O3A GDP 200 A 1 
HETATM 6 P PA GDP . . . F 4 8.03 -15.181 -43.608 1 60.89 ? PA GDP 200 A 1 
HETATM 7 O O1A GDP . . . F 4 8.467 -15.167 -42.156 1 62.29 ? O1A GDP 200 A 1 
HETATM 8 O O2A GDP . . . F 4 8.355 -16.468 -44.296 1 60.45 ? O2A GDP 200 A 1 
HETATM 9 O O5' GDP . . . F 4 8.721 -13.893 -44.25 1 65.85 ? O5' GDP 200 A 1 
HETATM 10 C C5' GDP . . . F 4 8.071 -13.295 -45.379 1 69.17 ? C5' GDP 200 A 1 
HETATM 11 C C4' GDP . . . F 4 8.957 -12.218 -45.945 1 71.08 ? C4' GDP 200 A 1 
HETATM 12 O O4' GDP . . . F 4 8.966 -11.187 -44.975 1 72.92 ? O4' GDP 200 A 1 
HETATM 13 C C3' GDP . . . F 4 10.403 -12.63 -46.107 1 73.62 ? C3' GDP 200 A 1 
HETATM 14 O O3' GDP . . . F 4 10.934 -12.02 -47.277 1 74.11 ? O3' GDP 200 A 1 
HETATM 15 C C2' GDP . . . F 4 11.098 -12.075 -44.881 1 75.59 ? C2' GDP 200 A 1 
HETATM 16 O O2' GDP . . . F 4 12.479 -11.743 -45.081 1 77.27 ? O2' GDP 200 A 1 
HETATM 17 C C1' GDP . . . F 4 10.28 -10.846 -44.6 1 75.56 ? C1' GDP 200 A 1 
HETATM 18 N N9 GDP . . . F 4 10.31 -10.508 -43.181 1 75.99 ? N9 GDP 200 A 1 
HETATM 19 C C8 GDP . . . F 4 9.889 -11.262 -42.158 1 77.15 ? C8 GDP 200 A 1 
HETATM 20 N N7 GDP . . . F 4 10.062 -10.603 -40.972 1 77.07 ? N7 GDP 200 A 1 
HETATM 21 C C5 GDP . . . F 4 10.593 -9.409 -41.253 1 76.33 ? C5 GDP 200 A 1 
HETATM 22 C C6 GDP . . . F 4 11.037 -8.234 -40.488 1 76.4 ? C6 GDP 200 A 1 
HETATM 23 O O6 GDP . . . F 4 10.965 -8.174 -39.247 1 76.6 ? O6 GDP 200 A 1 
HETATM 24 N N1 GDP . . . F 4 11.533 -7.219 -41.184 1 77.04 ? N1 GDP 200 A 1 
HETATM 25 C C2 GDP . . . F 4 11.635 -7.251 -42.528 1 77.04 ? C2 GDP 200 A 1 
HETATM 26 N N2 GDP . . . F 4 12.15 -6.184 -43.171 1 77.62 ? N2 GDP 200 A 1 
HETATM 27 N N3 GDP . . . F 4 11.256 -8.286 -43.295 1 76.3 ? N3 GDP 200 A 1 
HETATM 28 C C4 GDP . . . F 4 10.751 -9.37 -42.709 1 76.22 ? C4 GDP 200 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           318 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           28 
#