data_6BT0
#
_model_server_result.job_id            svyjia6ev-2fh-Qt3cYUnw 
_model_server_result.datetime_utc      '2024-11-29 03:33:34' 
_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          6bt0 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":202}' 
#
_entry.id    6BT0 
#
_exptl.entry_id    6BT0 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          3 
_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         68.35 
_cell.angle_beta          90.01 
_cell.angle_gamma         72.05 
_cell.entry_id            6BT0 
_cell.length_a            49.15 
_cell.length_b            60.14 
_cell.length_c            66.32 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6BT0 
_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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,N 1 1 
B,G,H,I,O 2 1 
C,J,K,P 3 1 
D,L,M,Q 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
? 3 F N N 
? 3 H N N 
? 3 K N N 
? 3 M 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 OG SER 21 A SER 20 1_555 E MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? 
metalc ? metalc2 E MG MG . A MG 201 1_555 F O1B GDP . A GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? 
metalc ? metalc3 E MG MG . A MG 201 1_555 N O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? 
metalc ? metalc4 E MG MG . A MG 201 1_555 N O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? 
metalc ? metalc5 E MG MG . A MG 201 1_555 N O HOH . A HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? 
metalc ? metalc6 E MG MG . A MG 201 1_555 N O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? 
metalc ? metalc7 B OG SER 21 B SER 20 1_555 G MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? 
metalc ? metalc8 G MG MG . B MG 201 1_555 H O3B GDP . B GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? 
metalc ? metalc9 G MG MG . B MG 201 1_555 O O HOH . B HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? 
metalc ? metalc10 G MG MG . B MG 201 1_555 O O HOH . B HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? 
metalc ? metalc11 G MG MG . B MG 201 1_555 O O HOH . B HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.618 ? 
metalc ? metalc12 G MG MG . B MG 201 1_555 O O HOH . B HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? 
metalc ? metalc13 C OG SER 21 C SER 20 1_555 J MG MG . C MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
metalc ? metalc14 J MG MG . C MG 201 1_555 K O1B GDP . C GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? 
metalc ? metalc15 J MG MG . C MG 201 1_555 P O HOH . C HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? 
metalc ? metalc16 J MG MG . C MG 201 1_555 P O HOH . C HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.912 ? 
metalc ? metalc17 J MG MG . C MG 201 1_555 P O HOH . C HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.763 ? 
metalc ? metalc18 D OG SER 21 D SER 20 1_555 L MG MG . D MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? 
metalc ? metalc19 L MG MG . D MG 201 1_555 M O3B GDP . D GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? 
metalc ? metalc20 L MG MG . D MG 201 1_555 M O2B GDP . D GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.969 ? 
metalc ? metalc21 L MG MG . D MG 201 1_555 Q O HOH . D HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.932 ? 
metalc ? metalc22 L MG MG . D MG 201 1_555 Q O HOH . D HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.922 ? 
metalc ? metalc23 L MG MG . D MG 201 1_555 Q O HOH . D HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
#
_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 126 n n 
PB O2B GDP sing 127 n n 
PB O3B GDP sing 128 n n 
PB O3A GDP sing 129 n n 
O2B HOB2 GDP sing 130 n n 
O3B HOB3 GDP sing 131 n n 
O3A PA GDP sing 132 n n 
PA O1A GDP doub 133 n n 
PA O2A GDP sing 134 n n 
PA O5' GDP sing 135 n n 
O2A HOA2 GDP sing 136 n n 
O5' C5' GDP sing 137 n n 
C5' C4' GDP sing 138 n n 
C5' H5' GDP sing 139 n n 
C5' "H5''" GDP sing 140 n n 
C4' O4' GDP sing 141 n n 
C4' C3' GDP sing 142 n n 
C4' H4' GDP sing 143 n n 
O4' C1' GDP sing 144 n n 
C3' O3' GDP sing 145 n n 
C3' C2' GDP sing 146 n n 
C3' H3' GDP sing 147 n n 
O3' HO3' GDP sing 148 n n 
C2' O2' GDP sing 149 n n 
C2' C1' GDP sing 150 n n 
C2' H2' GDP sing 151 n n 
O2' HO2' GDP sing 152 n n 
C1' N9 GDP sing 153 n n 
C1' H1' GDP sing 154 n n 
N9 C8 GDP sing 155 n y 
N9 C4 GDP sing 156 n y 
C8 N7 GDP doub 157 n y 
C8 H8 GDP sing 158 n n 
N7 C5 GDP sing 159 n y 
C5 C6 GDP sing 160 n n 
C5 C4 GDP doub 161 n y 
C6 O6 GDP doub 162 n n 
C6 N1 GDP sing 163 n n 
N1 C2 GDP sing 164 n n 
N1 HN1 GDP sing 165 n n 
C2 N2 GDP sing 166 n n 
C2 N3 GDP doub 167 n n 
N2 HN21 GDP sing 168 n n 
N2 HN22 GDP sing 169 n n 
N3 C4 GDP sing 170 n n 
#
_atom_sites.entry_id                     6BT0 
_atom_sites.fract_transf_matrix[1][1]    0.020346 
_atom_sites.fract_transf_matrix[1][2]    -0.006591 
_atom_sites.fract_transf_matrix[1][3]    0.002776 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.017479 
_atom_sites.fract_transf_matrix[2][3]    -0.007354 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.016359 
_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 2 MG A 1 201 202 MG MG . 
F 3 GDP A 1 202 201 GDP GDP . 
G 2 MG B 1 201 202 MG MG . 
H 3 GDP B 1 202 201 GDP GDP . 
I 4 E7V B 1 203 1 E7V NV1 . 
J 2 MG C 1 201 202 MG MG . 
K 3 GDP C 1 202 201 GDP GDP . 
L 2 MG D 1 201 202 MG MG . 
M 3 GDP D 1 202 201 GDP GDP . 
N 5 HOH A 1 301 3 HOH HOH . 
N 5 HOH A 2 302 2 HOH HOH . 
N 5 HOH A 3 303 1 HOH HOH . 
N 5 HOH A 4 304 4 HOH HOH . 
O 5 HOH B 1 301 7 HOH HOH . 
O 5 HOH B 2 302 13 HOH HOH . 
O 5 HOH B 3 303 11 HOH HOH . 
O 5 HOH B 4 304 5 HOH HOH . 
O 5 HOH B 5 305 14 HOH HOH . 
O 5 HOH B 6 306 12 HOH HOH . 
P 5 HOH C 1 301 8 HOH HOH . 
P 5 HOH C 2 302 6 HOH HOH . 
P 5 HOH C 3 303 9 HOH HOH . 
P 5 HOH C 4 304 10 HOH HOH . 
Q 5 HOH D 1 301 18 HOH HOH . 
Q 5 HOH D 2 302 15 HOH HOH . 
Q 5 HOH D 3 303 17 HOH HOH . 
Q 5 HOH D 4 304 16 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 3 6.848 -1.909 -6.367 1 28.19 ? PB GDP 202 A 1 
HETATM 2 O O1B GDP . . . F 3 5.606 -1.478 -7.115 1 26.36 ? O1B GDP 202 A 1 
HETATM 3 O O2B GDP . . . F 3 6.882 -1.541 -4.892 1 27.07 ? O2B GDP 202 A 1 
HETATM 4 O O3B GDP . . . F 3 8.099 -1.543 -7.091 1 26.11 ? O3B GDP 202 A 1 
HETATM 5 O O3A GDP . . . F 3 6.77 -3.538 -6.363 1 26.63 ? O3A GDP 202 A 1 
HETATM 6 P PA GDP . . . F 3 5.994 -4.363 -7.523 1 25.08 ? PA GDP 202 A 1 
HETATM 7 O O1A GDP . . . F 3 6.512 -3.764 -8.804 1 23.96 ? O1A GDP 202 A 1 
HETATM 8 O O2A GDP . . . F 3 4.526 -4.348 -7.215 1 24.76 ? O2A GDP 202 A 1 
HETATM 9 O O5' GDP . . . F 3 6.494 -5.877 -7.414 1 23.52 ? O5' GDP 202 A 1 
HETATM 10 C C5' GDP . . . F 3 7.891 -6.044 -7.163 1 23.27 ? C5' GDP 202 A 1 
HETATM 11 C C4' GDP . . . F 3 8.408 -7.424 -7.543 1 22.71 ? C4' GDP 202 A 1 
HETATM 12 O O4' GDP . . . F 3 8.073 -8.371 -6.546 1 21.76 ? O4' GDP 202 A 1 
HETATM 13 C C3' GDP . . . F 3 7.812 -7.962 -8.821 1 22.97 ? C3' GDP 202 A 1 
HETATM 14 O O3' GDP . . . F 3 8.806 -8.804 -9.442 1 22.65 ? O3' GDP 202 A 1 
HETATM 15 C C2' GDP . . . F 3 6.614 -8.741 -8.36 1 22.24 ? C2' GDP 202 A 1 
HETATM 16 O O2' GDP . . . F 3 6.354 -9.747 -9.327 1 22.97 ? O2' GDP 202 A 1 
HETATM 17 C C1' GDP . . . F 3 7.076 -9.27 -7.008 1 22.69 ? C1' GDP 202 A 1 
HETATM 18 N N9 GDP . . . F 3 6.048 -9.379 -5.93 1 23.65 ? N9 GDP 202 A 1 
HETATM 19 C C8 GDP . . . F 3 5.29 -8.395 -5.42 1 24.43 ? C8 GDP 202 A 1 
HETATM 20 N N7 GDP . . . F 3 4.462 -8.849 -4.438 1 24.13 ? N7 GDP 202 A 1 
HETATM 21 C C5 GDP . . . F 3 4.705 -10.143 -4.305 1 23.33 ? C5 GDP 202 A 1 
HETATM 22 C C6 GDP . . . F 3 4.211 -11.209 -3.44 1 24.59 ? C6 GDP 202 A 1 
HETATM 23 O O6 GDP . . . F 3 3.328 -10.993 -2.582 1 27.51 ? O6 GDP 202 A 1 
HETATM 24 N N1 GDP . . . F 3 4.724 -12.43 -3.595 1 24.88 ? N1 GDP 202 A 1 
HETATM 25 C C2 GDP . . . F 3 5.67 -12.721 -4.5 1 25.1 ? C2 GDP 202 A 1 
HETATM 26 N N2 GDP . . . F 3 6.13 -14.001 -4.597 1 25.47 ? N2 GDP 202 A 1 
HETATM 27 N N3 GDP . . . F 3 6.194 -11.761 -5.317 1 24.94 ? N3 GDP 202 A 1 
HETATM 28 C C4 GDP . . . F 3 5.753 -10.486 -5.261 1 23.75 ? C4 GDP 202 A 1 
#
_model_server_stats.io_time_ms              108 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           254 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           28 
#