data_6B9G
#
_model_server_result.job_id            0sbfM4ejKgsNGOdcfwNUqQ 
_model_server_result.datetime_utc      '2024-12-13 13:39:01' 
_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          6b9g 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":401}' 
#
_entry.id    6B9G 
#
_exptl.entry_id    6B9G 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          2 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            6B9G 
_cell.length_a            308.032 
_cell.length_b            308.032 
_cell.length_c            308.032 
_cell.Z_PDB               192 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6B9G 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        196 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'F 2 3' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
PISA monomeric 1 author_and_software_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,M 1 1 
B,G,H,N 2 1 
C,I,J,O 3 1 
D,K,L,P 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
? 2 E N N 
? 2 G N N 
? 2 I N N 
? 2 K 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 OD2 ASP 147 B ASP 146 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? 
metalc ? metalc2 B OD2 ASP 147 C ASP 146 1_555 H MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.594 ? 
metalc ? metalc3 C OG SER 82 D SER 81 1_555 J MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.973 ? 
metalc ? metalc4 I O3B GDP . D GDP 401 1_555 J MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.907 ? 
metalc ? metalc5 L MG MG . A MG 402 1_555 P O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.979 ? 
metalc ? metalc6 L MG MG . A MG 402 1_555 P O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? 
metalc ? metalc7 L MG MG . A MG 402 1_555 P O HOH . A HOH 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? 
#
_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                     6B9G 
_atom_sites.fract_transf_matrix[1][1]    0.003246 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.003246 
_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]    0.003246 
_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 GDP B 1 401 2 GDP GDP . 
F 3 MG B 1 402 2 MG MG . 
G 2 GDP C 1 401 3 GDP GDP . 
H 3 MG C 1 402 3 MG MG . 
I 2 GDP D 1 401 4 GDP GDP . 
J 3 MG D 1 402 15 MG MG . 
K 2 GDP A 1 401 1 GDP GDP . 
L 3 MG A 1 402 1 MG MG . 
M 4 HOH B 1 501 119 HOH HOH . 
M 4 HOH B 2 502 1 HOH HOH . 
M 4 HOH B 3 503 60 HOH HOH . 
M 4 HOH B 4 504 116 HOH HOH . 
M 4 HOH B 5 505 57 HOH HOH . 
M 4 HOH B 6 506 5 HOH HOH . 
M 4 HOH B 7 507 117 HOH HOH . 
M 4 HOH B 8 508 112 HOH HOH . 
M 4 HOH B 9 509 132 HOH HOH . 
M 4 HOH B 10 510 109 HOH HOH . 
M 4 HOH B 11 511 43 HOH HOH . 
M 4 HOH B 12 512 106 HOH HOH . 
M 4 HOH B 13 513 44 HOH HOH . 
M 4 HOH B 14 514 74 HOH HOH . 
M 4 HOH B 15 515 135 HOH HOH . 
M 4 HOH B 16 516 137 HOH HOH . 
M 4 HOH B 17 517 82 HOH HOH . 
M 4 HOH B 18 518 76 HOH HOH . 
M 4 HOH B 19 519 75 HOH HOH . 
M 4 HOH B 20 520 93 HOH HOH . 
M 4 HOH B 21 521 83 HOH HOH . 
M 4 HOH B 22 522 91 HOH HOH . 
M 4 HOH B 23 523 22 HOH HOH . 
M 4 HOH B 24 524 120 HOH HOH . 
M 4 HOH B 25 525 107 HOH HOH . 
M 4 HOH B 26 526 73 HOH HOH . 
M 4 HOH B 27 527 28 HOH HOH . 
M 4 HOH B 28 528 134 HOH HOH . 
M 4 HOH B 29 529 29 HOH HOH . 
M 4 HOH B 30 530 17 HOH HOH . 
M 4 HOH B 31 531 23 HOH HOH . 
M 4 HOH B 32 532 84 HOH HOH . 
M 4 HOH B 33 533 126 HOH HOH . 
M 4 HOH B 34 534 121 HOH HOH . 
N 4 HOH C 1 501 4 HOH HOH . 
N 4 HOH C 2 502 71 HOH HOH . 
N 4 HOH C 3 503 129 HOH HOH . 
N 4 HOH C 4 504 138 HOH HOH . 
N 4 HOH C 5 505 72 HOH HOH . 
N 4 HOH C 6 506 89 HOH HOH . 
N 4 HOH C 7 507 6 HOH HOH . 
N 4 HOH C 8 508 56 HOH HOH . 
N 4 HOH C 9 509 103 HOH HOH . 
N 4 HOH C 10 510 122 HOH HOH . 
N 4 HOH C 11 511 34 HOH HOH . 
N 4 HOH C 12 512 108 HOH HOH . 
N 4 HOH C 13 513 133 HOH HOH . 
N 4 HOH C 14 514 105 HOH HOH . 
N 4 HOH C 15 515 59 HOH HOH . 
N 4 HOH C 16 516 27 HOH HOH . 
N 4 HOH C 17 517 58 HOH HOH . 
N 4 HOH C 18 518 13 HOH HOH . 
N 4 HOH C 19 519 32 HOH HOH . 
N 4 HOH C 20 520 110 HOH HOH . 
N 4 HOH C 21 521 16 HOH HOH . 
N 4 HOH C 22 522 38 HOH HOH . 
N 4 HOH C 23 523 33 HOH HOH . 
N 4 HOH C 24 524 131 HOH HOH . 
N 4 HOH C 25 525 37 HOH HOH . 
N 4 HOH C 26 526 10 HOH HOH . 
N 4 HOH C 27 527 87 HOH HOH . 
N 4 HOH C 28 528 125 HOH HOH . 
N 4 HOH C 29 529 139 HOH HOH . 
N 4 HOH C 30 530 41 HOH HOH . 
O 4 HOH D 1 501 3 HOH HOH . 
O 4 HOH D 2 502 127 HOH HOH . 
O 4 HOH D 3 503 26 HOH HOH . 
O 4 HOH D 4 504 66 HOH HOH . 
O 4 HOH D 5 505 115 HOH HOH . 
O 4 HOH D 6 506 113 HOH HOH . 
O 4 HOH D 7 507 14 HOH HOH . 
O 4 HOH D 8 508 130 HOH HOH . 
O 4 HOH D 9 509 31 HOH HOH . 
O 4 HOH D 10 510 124 HOH HOH . 
O 4 HOH D 11 511 78 HOH HOH . 
P 4 HOH A 1 501 101 HOH HOH . 
P 4 HOH A 2 502 2 HOH HOH . 
P 4 HOH A 3 503 99 HOH HOH . 
P 4 HOH A 4 504 123 HOH HOH . 
P 4 HOH A 5 505 20 HOH HOH . 
P 4 HOH A 6 506 136 HOH HOH . 
P 4 HOH A 7 507 46 HOH HOH . 
P 4 HOH A 8 508 111 HOH HOH . 
P 4 HOH A 9 509 104 HOH HOH . 
P 4 HOH A 10 510 42 HOH HOH . 
P 4 HOH A 11 511 81 HOH HOH . 
P 4 HOH A 12 512 118 HOH HOH . 
P 4 HOH A 13 513 54 HOH HOH . 
P 4 HOH A 14 514 12 HOH HOH . 
P 4 HOH A 15 515 114 HOH HOH . 
P 4 HOH A 16 516 102 HOH HOH . 
P 4 HOH A 17 517 100 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 . . . E 2 62.608 -20.557 -36.212 1 49.35 ? PB GDP 401 B 1 
HETATM 2 O O1B GDP . . . E 2 63.839 -19.716 -36.449 1 65.54 ? O1B GDP 401 B 1 
HETATM 3 O O2B GDP . . . E 2 62.965 -21.702 -35.299 1 29.52 ? O2B GDP 401 B 1 
HETATM 4 O O3B GDP . . . E 2 61.533 -19.73 -35.554 1 52.03 ? O3B GDP 401 B 1 
HETATM 5 O O3A GDP . . . E 2 62.084 -21.11 -37.629 1 56.8 ? O3A GDP 401 B 1 
HETATM 6 P PA GDP . . . E 2 60.674 -21.872 -37.796 1 47.64 ? PA GDP 401 B 1 
HETATM 7 O O1A GDP . . . E 2 59.616 -20.937 -38.332 1 73.42 ? O1A GDP 401 B 1 
HETATM 8 O O2A GDP . . . E 2 60.198 -22.504 -36.517 1 32.95 ? O2A GDP 401 B 1 
HETATM 9 O O5' GDP . . . E 2 61.04 -22.999 -38.879 1 50.67 ? O5' GDP 401 B 1 
HETATM 10 C C5' GDP . . . E 2 61.316 -24.321 -38.429 1 49.29 ? C5' GDP 401 B 1 
HETATM 11 C C4' GDP . . . E 2 60.96 -25.321 -39.514 1 42.53 ? C4' GDP 401 B 1 
HETATM 12 O O4' GDP . . . E 2 60.726 -26.565 -38.863 1 50.36 ? O4' GDP 401 B 1 
HETATM 13 C C3' GDP . . . E 2 59.662 -24.942 -40.189 1 43 ? C3' GDP 401 B 1 
HETATM 14 O O3' GDP . . . E 2 59.643 -25.487 -41.51 1 38.18 ? O3' GDP 401 B 1 
HETATM 15 C C2' GDP . . . E 2 58.605 -25.624 -39.355 1 43.64 ? C2' GDP 401 B 1 
HETATM 16 O O2' GDP . . . E 2 57.502 -26.02 -40.172 1 52.65 ? O2' GDP 401 B 1 
HETATM 17 C C1' GDP . . . E 2 59.325 -26.833 -38.783 1 47.04 ? C1' GDP 401 B 1 
HETATM 18 N N9 GDP . . . E 2 58.976 -27.029 -37.359 1 43.05 ? N9 GDP 401 B 1 
HETATM 19 C C8 GDP . . . E 2 58.266 -26.197 -36.574 1 42.86 ? C8 GDP 401 B 1 
HETATM 20 N N7 GDP . . . E 2 58.157 -26.698 -35.315 1 48.85 ? N7 GDP 401 B 1 
HETATM 21 C C5 GDP . . . E 2 58.825 -27.867 -35.287 1 47.62 ? C5 GDP 401 B 1 
HETATM 22 C C6 GDP . . . E 2 59.12 -28.913 -34.282 1 48.85 ? C6 GDP 401 B 1 
HETATM 23 O O6 GDP . . . E 2 58.695 -28.814 -33.112 1 54.54 ? O6 GDP 401 B 1 
HETATM 24 N N1 GDP . . . E 2 59.851 -29.968 -34.667 1 51.63 ? N1 GDP 401 B 1 
HETATM 25 C C2 GDP . . . E 2 60.32 -30.105 -35.922 1 41.09 ? C2 GDP 401 B 1 
HETATM 26 N N2 GDP . . . E 2 61.052 -31.201 -36.232 1 30.67 ? N2 GDP 401 B 1 
HETATM 27 N N3 GDP . . . E 2 60.092 -29.187 -36.892 1 44.9 ? N3 GDP 401 B 1 
HETATM 28 C C4 GDP . . . E 2 59.367 -28.074 -36.635 1 47.8 ? C4 GDP 401 B 1 
#
_model_server_stats.io_time_ms              36 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           285 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#