data_4F61
#
_model_server_result.job_id            0TuD5HmVxVQkEa59FrZGgg 
_model_server_result.datetime_utc      '2024-11-22 23:04:59' 
_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          4f61 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":600}' 
#
_entry.id    4F61 
#
_exptl.entry_id    4F61 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          6 
_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          92.02 
_cell.angle_gamma         90 
_cell.entry_id            4F61 
_cell.length_a            639.74 
_cell.length_b            66.1 
_cell.length_c            128.13 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4F61 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    nonameric 
_pdbx_struct_assembly.oligomeric_count      9 
_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,I,J,K,L,M,N,O,P,Q,R,S,T,U 
_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
? 6 L N N 
? 6 O N N 
? 6 R N N 
? 6 U 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 OE2 GLU 71 A GLU 71 1_555 K MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? 
metalc ? metalc2 A OE1 GLU 71 A GLU 71 1_555 K MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? 
metalc ? metalc3 J O1G GTP . A GTP 600 1_555 K MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
metalc ? metalc4 J O1B GTP . A GTP 600 1_555 K MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc5 C OE2 GLU 71 C GLU 71 1_555 N MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? 
metalc ? metalc6 C OE1 GLU 71 C GLU 71 1_555 N MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? 
metalc ? metalc7 M O1G GTP . C GTP 600 1_555 N MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
metalc ? metalc8 M O1B GTP . C GTP 600 1_555 N MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
metalc ? metalc9 E OE2 GLU 71 E GLU 71 1_555 Q MG MG . E MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? 
metalc ? metalc10 E OE1 GLU 71 E GLU 71 1_555 Q MG MG . E MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? 
metalc ? metalc11 P O1G GTP . E GTP 600 1_555 Q MG MG . E MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
metalc ? metalc12 P O1B GTP . E GTP 600 1_555 Q MG MG . E MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? 
metalc ? metalc13 G OE2 GLU 71 G GLU 71 1_555 T MG MG . G MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? 
metalc ? metalc14 G OE1 GLU 71 G GLU 71 1_555 T MG MG . G MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.533 ? 
metalc ? metalc15 S O1G GTP . G GTP 600 1_555 T MG MG . G MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? 
metalc ? metalc16 S O1B GTP . G GTP 600 1_555 T MG MG . G MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? 
#
_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                     4F61 
_atom_sites.fract_transf_matrix[1][1]    0.001563 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000055 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015129 
_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]    0.007809 
_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
J 4 GTP A 1 600 600 GTP GTP . 
K 5 MG A 1 601 601 MG MG . 
L 6 GDP B 1 600 600 GDP GDP . 
M 4 GTP C 1 600 600 GTP GTP . 
N 5 MG C 1 601 601 MG MG . 
O 6 GDP D 1 600 600 GDP GDP . 
P 4 GTP E 1 600 600 GTP GTP . 
Q 5 MG E 1 601 601 MG MG . 
R 6 GDP F 1 600 600 GDP GDP . 
S 4 GTP G 1 600 600 GTP GTP . 
T 5 MG G 1 601 601 MG MG . 
U 6 GDP H 1 600 600 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 . . . L 6 -86.939 7.823 22.883 1 122.8 ? PB GDP 600 B 1 
HETATM 2 O O1B GDP . . . L 6 -88.09 6.799 22.615 1 117.6 ? O1B GDP 600 B 1 
HETATM 3 O O2B GDP . . . L 6 -87.269 8.882 23.97 1 126.14 ? O2B GDP 600 B 1 
HETATM 4 O O3B GDP . . . L 6 -85.632 7.16 23.331 1 124.6 ? O3B GDP 600 B 1 
HETATM 5 O O3A GDP . . . L 6 -86.718 8.608 21.514 1 124.07 ? O3A GDP 600 B 1 
HETATM 6 P PA GDP . . . L 6 -87.71 9.326 20.502 1 123.04 ? PA GDP 600 B 1 
HETATM 7 O O1A GDP . . . L 6 -87.431 10.784 20.577 1 128.36 ? O1A GDP 600 B 1 
HETATM 8 O O2A GDP . . . L 6 -89.167 8.869 20.835 1 118.76 ? O2A GDP 600 B 1 
HETATM 9 O O5' GDP . . . L 6 -87.282 8.731 19.096 1 122.22 ? O5' GDP 600 B 1 
HETATM 10 C C5' GDP . . . L 6 -86.86 9.478 17.939 1 125.96 ? C5' GDP 600 B 1 
HETATM 11 C C4' GDP . . . L 6 -87.797 9.131 16.803 1 123.35 ? C4' GDP 600 B 1 
HETATM 12 O O4' GDP . . . L 6 -89.137 9.55 17.152 1 121.85 ? O4' GDP 600 B 1 
HETATM 13 C C3' GDP . . . L 6 -87.493 9.845 15.489 1 127.8 ? C3' GDP 600 B 1 
HETATM 14 O O3' GDP . . . L 6 -87.997 9.117 14.373 1 126.04 ? O3' GDP 600 B 1 
HETATM 15 C C2' GDP . . . L 6 -88.226 11.169 15.679 1 130.73 ? C2' GDP 600 B 1 
HETATM 16 O O2' GDP . . . L 6 -88.481 11.788 14.42 1 134.15 ? O2' GDP 600 B 1 
HETATM 17 C C1' GDP . . . L 6 -89.504 10.675 16.373 1 125.66 ? C1' GDP 600 B 1 
HETATM 18 N N9 GDP . . . L 6 -90.214 11.648 17.237 1 127.25 ? N9 GDP 600 B 1 
HETATM 19 C C8 GDP . . . L 6 -89.789 12.237 18.406 1 129.81 ? C8 GDP 600 B 1 
HETATM 20 N N7 GDP . . . L 6 -90.705 12.983 18.975 1 131.18 ? N7 GDP 600 B 1 
HETATM 21 C C5 GDP . . . L 6 -91.802 12.886 18.134 1 129.43 ? C5 GDP 600 B 1 
HETATM 22 C C6 GDP . . . L 6 -93.122 13.462 18.209 1 130.24 ? C6 GDP 600 B 1 
HETATM 23 O O6 GDP . . . L 6 -93.55 14.179 19.112 1 132.87 ? O6 GDP 600 B 1 
HETATM 24 N N1 GDP . . . L 6 -93.93 13.103 17.132 1 128.53 ? N1 GDP 600 B 1 
HETATM 25 C C2 GDP . . . L 6 -93.548 12.282 16.097 1 126.33 ? C2 GDP 600 B 1 
HETATM 26 N N2 GDP . . . L 6 -94.449 12.047 15.138 1 125.66 ? N2 GDP 600 B 1 
HETATM 27 N N3 GDP . . . L 6 -92.336 11.73 16.011 1 125.58 ? N3 GDP 600 B 1 
HETATM 28 C C4 GDP . . . L 6 -91.514 12.07 17.053 1 126.95 ? C4 GDP 600 B 1 
#
_model_server_stats.io_time_ms              57 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    31 
_model_server_stats.query_time_ms           265 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#