data_3QOF
#
_model_server_result.job_id            JVMi2EcJXhG9gKiESzsOeQ 
_model_server_result.datetime_utc      '2024-12-23 07:07:10' 
_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          3qof 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":593}' 
#
_entry.id    3QOF 
#
_exptl.entry_id    3QOF 
_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            3QOF 
_cell.length_a            104.742 
_cell.length_b            133.445 
_cell.length_c            176.266 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3QOF 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 OG SER 93 A SER 81 1_555 F MG MG . A MG 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? 
metalc ? metalc2 E O2B GDP . A GDP 593 1_555 F MG MG . A MG 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.791 ? 
metalc ? metalc3 G O2B GDP . B GDP 593 1_555 H MG MG . B MG 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? 
metalc ? metalc4 C OG SER 93 C SER 81 1_555 J MG MG . C MG 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.779 ? 
metalc ? metalc5 I O2B GDP . C GDP 593 1_555 J MG MG . C MG 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? 
metalc ? metalc6 D OG SER 93 D SER 81 1_555 L MG MG . D MG 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.992 ? 
metalc ? metalc7 K O2B GDP . D GDP 593 1_555 L MG MG . D MG 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.888 ? 
#
_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                     3QOF 
_atom_sites.fract_transf_matrix[1][1]    0.009547 
_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]    0.007494 
_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]    0.005673 
_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 A 1 593 593 GDP GDP . 
F 3 MG A 1 595 595 MG MG . 
G 2 GDP B 1 593 593 GDP GDP . 
H 3 MG B 1 595 595 MG MG . 
I 2 GDP C 1 593 593 GDP GDP . 
J 3 MG C 1 595 595 MG MG . 
K 2 GDP D 1 593 593 GDP GDP . 
L 3 MG D 1 595 595 MG MG . 
M 4 HOH A 1 448 3 HOH HOH . 
M 4 HOH A 2 449 5 HOH HOH . 
M 4 HOH A 3 450 9 HOH HOH . 
M 4 HOH A 4 451 14 HOH HOH . 
M 4 HOH A 5 452 18 HOH HOH . 
M 4 HOH A 6 453 30 HOH HOH . 
M 4 HOH A 7 454 31 HOH HOH . 
M 4 HOH A 8 455 32 HOH HOH . 
M 4 HOH A 9 456 35 HOH HOH . 
M 4 HOH A 10 457 36 HOH HOH . 
M 4 HOH A 11 458 37 HOH HOH . 
M 4 HOH A 12 459 39 HOH HOH . 
M 4 HOH A 13 460 40 HOH HOH . 
M 4 HOH A 14 461 46 HOH HOH . 
M 4 HOH A 15 462 47 HOH HOH . 
M 4 HOH A 16 463 50 HOH HOH . 
M 4 HOH A 17 464 52 HOH HOH . 
M 4 HOH A 18 465 61 HOH HOH . 
M 4 HOH A 19 466 62 HOH HOH . 
M 4 HOH A 20 467 71 HOH HOH . 
M 4 HOH A 21 468 72 HOH HOH . 
M 4 HOH A 22 469 74 HOH HOH . 
M 4 HOH A 23 470 76 HOH HOH . 
M 4 HOH A 24 471 78 HOH HOH . 
M 4 HOH A 25 472 84 HOH HOH . 
M 4 HOH A 26 473 91 HOH HOH . 
M 4 HOH A 27 474 93 HOH HOH . 
M 4 HOH A 28 475 98 HOH HOH . 
M 4 HOH A 29 476 99 HOH HOH . 
M 4 HOH A 30 477 100 HOH HOH . 
M 4 HOH A 31 478 102 HOH HOH . 
M 4 HOH A 32 479 118 HOH HOH . 
M 4 HOH A 33 480 119 HOH HOH . 
M 4 HOH A 34 481 120 HOH HOH . 
M 4 HOH A 35 482 123 HOH HOH . 
M 4 HOH A 36 483 125 HOH HOH . 
M 4 HOH A 37 484 126 HOH HOH . 
N 4 HOH B 1 448 6 HOH HOH . 
N 4 HOH B 2 449 8 HOH HOH . 
N 4 HOH B 3 450 16 HOH HOH . 
N 4 HOH B 4 451 19 HOH HOH . 
N 4 HOH B 5 452 25 HOH HOH . 
N 4 HOH B 6 453 33 HOH HOH . 
N 4 HOH B 7 454 34 HOH HOH . 
N 4 HOH B 8 455 38 HOH HOH . 
N 4 HOH B 9 456 44 HOH HOH . 
N 4 HOH B 10 457 45 HOH HOH . 
N 4 HOH B 11 458 54 HOH HOH . 
N 4 HOH B 12 459 57 HOH HOH . 
N 4 HOH B 13 460 63 HOH HOH . 
N 4 HOH B 14 461 64 HOH HOH . 
N 4 HOH B 15 462 70 HOH HOH . 
N 4 HOH B 16 463 80 HOH HOH . 
N 4 HOH B 17 464 81 HOH HOH . 
N 4 HOH B 18 465 85 HOH HOH . 
N 4 HOH B 19 466 86 HOH HOH . 
N 4 HOH B 20 467 89 HOH HOH . 
N 4 HOH B 21 468 94 HOH HOH . 
N 4 HOH B 22 469 96 HOH HOH . 
N 4 HOH B 23 470 107 HOH HOH . 
N 4 HOH B 24 471 109 HOH HOH . 
N 4 HOH B 25 472 110 HOH HOH . 
N 4 HOH B 26 473 112 HOH HOH . 
N 4 HOH B 27 474 113 HOH HOH . 
N 4 HOH B 28 475 115 HOH HOH . 
N 4 HOH B 29 476 122 HOH HOH . 
O 4 HOH C 1 448 4 HOH HOH . 
O 4 HOH C 2 449 10 HOH HOH . 
O 4 HOH C 3 450 12 HOH HOH . 
O 4 HOH C 4 451 15 HOH HOH . 
O 4 HOH C 5 452 17 HOH HOH . 
O 4 HOH C 6 453 24 HOH HOH . 
O 4 HOH C 7 454 26 HOH HOH . 
O 4 HOH C 8 455 27 HOH HOH . 
O 4 HOH C 9 456 28 HOH HOH . 
O 4 HOH C 10 457 29 HOH HOH . 
O 4 HOH C 11 458 41 HOH HOH . 
O 4 HOH C 12 459 42 HOH HOH . 
O 4 HOH C 13 460 43 HOH HOH . 
O 4 HOH C 14 461 49 HOH HOH . 
O 4 HOH C 15 462 51 HOH HOH . 
O 4 HOH C 16 463 53 HOH HOH . 
O 4 HOH C 17 464 55 HOH HOH . 
O 4 HOH C 18 465 56 HOH HOH . 
O 4 HOH C 19 466 60 HOH HOH . 
O 4 HOH C 20 467 65 HOH HOH . 
O 4 HOH C 21 468 66 HOH HOH . 
O 4 HOH C 22 469 67 HOH HOH . 
O 4 HOH C 23 470 77 HOH HOH . 
O 4 HOH C 24 471 83 HOH HOH . 
O 4 HOH C 25 472 88 HOH HOH . 
O 4 HOH C 26 473 90 HOH HOH . 
O 4 HOH C 27 474 95 HOH HOH . 
O 4 HOH C 28 475 97 HOH HOH . 
O 4 HOH C 29 476 101 HOH HOH . 
O 4 HOH C 30 477 104 HOH HOH . 
O 4 HOH C 31 478 105 HOH HOH . 
O 4 HOH C 32 479 106 HOH HOH . 
O 4 HOH C 33 480 108 HOH HOH . 
O 4 HOH C 34 481 114 HOH HOH . 
O 4 HOH C 35 482 116 HOH HOH . 
O 4 HOH C 36 483 117 HOH HOH . 
O 4 HOH C 37 484 124 HOH HOH . 
P 4 HOH D 1 448 1 HOH HOH . 
P 4 HOH D 2 449 2 HOH HOH . 
P 4 HOH D 3 450 7 HOH HOH . 
P 4 HOH D 4 451 11 HOH HOH . 
P 4 HOH D 5 452 13 HOH HOH . 
P 4 HOH D 6 453 20 HOH HOH . 
P 4 HOH D 7 454 21 HOH HOH . 
P 4 HOH D 8 455 22 HOH HOH . 
P 4 HOH D 9 456 23 HOH HOH . 
P 4 HOH D 10 457 48 HOH HOH . 
P 4 HOH D 11 458 58 HOH HOH . 
P 4 HOH D 12 459 59 HOH HOH . 
P 4 HOH D 13 460 68 HOH HOH . 
P 4 HOH D 14 461 69 HOH HOH . 
P 4 HOH D 15 462 73 HOH HOH . 
P 4 HOH D 16 463 75 HOH HOH . 
P 4 HOH D 17 464 79 HOH HOH . 
P 4 HOH D 18 465 82 HOH HOH . 
P 4 HOH D 19 466 87 HOH HOH . 
P 4 HOH D 20 467 92 HOH HOH . 
P 4 HOH D 21 468 103 HOH HOH . 
P 4 HOH D 22 469 111 HOH HOH . 
P 4 HOH D 23 470 121 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 . . . K 2 -45.33 -21.027 -14.854 1 56.09 ? PB GDP 593 D 1 
HETATM 2 O O1B GDP . . . K 2 -45.456 -20.933 -13.353 1 47.4 ? O1B GDP 593 D 1 
HETATM 3 O O2B GDP . . . K 2 -45.033 -19.662 -15.432 1 69.07 ? O2B GDP 593 D 1 
HETATM 4 O O3B GDP . . . K 2 -44.159 -21.916 -15.153 1 69.78 ? O3B GDP 593 D 1 
HETATM 5 O O3A GDP . . . K 2 -46.571 -21.669 -15.671 1 59.13 ? O3A GDP 593 D 1 
HETATM 6 P PA GDP . . . K 2 -48.104 -21.673 -15.177 1 55.92 ? PA GDP 593 D 1 
HETATM 7 O O1A GDP . . . K 2 -48.18 -21.04 -13.823 1 51.72 ? O1A GDP 593 D 1 
HETATM 8 O O2A GDP . . . K 2 -48.997 -21.031 -16.217 1 54.23 ? O2A GDP 593 D 1 
HETATM 9 O O5' GDP . . . K 2 -48.513 -23.222 -15.043 1 61.73 ? O5' GDP 593 D 1 
HETATM 10 C C5' GDP . . . K 2 -48.709 -23.768 -13.741 1 55.61 ? C5' GDP 593 D 1 
HETATM 11 C C4' GDP . . . K 2 -49.707 -24.915 -13.794 1 54.06 ? C4' GDP 593 D 1 
HETATM 12 O O4' GDP . . . K 2 -50.313 -25.045 -12.507 1 54.9 ? O4' GDP 593 D 1 
HETATM 13 C C3' GDP . . . K 2 -50.868 -24.624 -14.715 1 57.59 ? C3' GDP 593 D 1 
HETATM 14 O O3' GDP . . . K 2 -51.503 -25.874 -14.976 1 57.73 ? O3' GDP 593 D 1 
HETATM 15 C C2' GDP . . . K 2 -51.817 -23.809 -13.872 1 51.88 ? C2' GDP 593 D 1 
HETATM 16 O O2' GDP . . . K 2 -53.156 -23.953 -14.351 1 47.45 ? O2' GDP 593 D 1 
HETATM 17 C C1' GDP . . . K 2 -51.629 -24.47 -12.517 1 49.29 ? C1' GDP 593 D 1 
HETATM 18 N N9 GDP . . . K 2 -51.706 -23.477 -11.426 1 49.62 ? N9 GDP 593 D 1 
HETATM 19 C C8 GDP . . . K 2 -51.897 -22.142 -11.523 1 43.95 ? C8 GDP 593 D 1 
HETATM 20 N N7 GDP . . . K 2 -51.901 -21.57 -10.28 1 40.83 ? N7 GDP 593 D 1 
HETATM 21 C C5 GDP . . . K 2 -51.701 -22.548 -9.372 1 40.53 ? C5 GDP 593 D 1 
HETATM 22 C C6 GDP . . . K 2 -51.585 -22.664 -7.895 1 40.21 ? C6 GDP 593 D 1 
HETATM 23 O O6 GDP . . . K 2 -51.673 -21.691 -7.122 1 42.54 ? O6 GDP 593 D 1 
HETATM 24 N N1 GDP . . . K 2 -51.368 -23.88 -7.385 1 48.11 ? N1 GDP 593 D 1 
HETATM 25 C C2 GDP . . . K 2 -51.26 -24.988 -8.146 1 45.61 ? C2 GDP 593 D 1 
HETATM 26 N N2 GDP . . . K 2 -51.047 -26.163 -7.516 1 35.58 ? N2 GDP 593 D 1 
HETATM 27 N N3 GDP . . . K 2 -51.359 -24.965 -9.499 1 40.81 ? N3 GDP 593 D 1 
HETATM 28 C C4 GDP . . . K 2 -51.565 -23.8 -10.143 1 44.34 ? C4 GDP 593 D 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           283 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           28 
#