data_6PTA
#
_model_server_result.job_id            lrXtZ5EuhrMapXp2m2Ndew 
_model_server_result.datetime_utc      '2024-12-22 06:21:18' 
_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          6pta 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":500}' 
#
_entry.id    6PTA 
#
_exptl.entry_id    6PTA 
_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          93.699 
_cell.angle_gamma         90 
_cell.entry_id            6PTA 
_cell.length_a            86.801 
_cell.length_b            42.285 
_cell.length_c            90.343 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PTA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        3 
_symmetry.space_group_name_Hall    'P 2y' 
_symmetry.space_group_name_H-M     'P 1 2 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
PISA dimeric 2 software_defined_assembly 1 
PISA dimeric 2 software_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,G,I,K 1 1 
B,D,F,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
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N N 
#
_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                     6PTA 
_atom_sites.fract_transf_matrix[1][1]    0.011521 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000745 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.023649 
_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]    0.011092 
_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 1 500 500 GDP GDP . 
F 2 GDP B 1 500 500 GDP GDP . 
G 2 GDP C 1 500 500 GDP GDP . 
H 2 GDP D 1 500 500 GDP GDP . 
I 3 HOH A 1 601 26 HOH HOH . 
I 3 HOH A 2 602 13 HOH HOH . 
I 3 HOH A 3 603 110 HOH HOH . 
I 3 HOH A 4 604 43 HOH HOH . 
I 3 HOH A 5 605 8 HOH HOH . 
I 3 HOH A 6 606 5 HOH HOH . 
I 3 HOH A 7 607 3 HOH HOH . 
I 3 HOH A 8 608 17 HOH HOH . 
I 3 HOH A 9 609 109 HOH HOH . 
I 3 HOH A 10 610 67 HOH HOH . 
I 3 HOH A 11 611 112 HOH HOH . 
I 3 HOH A 12 612 35 HOH HOH . 
I 3 HOH A 13 613 85 HOH HOH . 
I 3 HOH A 14 614 119 HOH HOH . 
I 3 HOH A 15 615 70 HOH HOH . 
I 3 HOH A 16 616 72 HOH HOH . 
I 3 HOH A 17 617 99 HOH HOH . 
I 3 HOH A 18 618 59 HOH HOH . 
I 3 HOH A 19 619 118 HOH HOH . 
I 3 HOH A 20 620 108 HOH HOH . 
I 3 HOH A 21 621 89 HOH HOH . 
I 3 HOH A 22 622 71 HOH HOH . 
I 3 HOH A 23 623 69 HOH HOH . 
I 3 HOH A 24 624 84 HOH HOH . 
I 3 HOH A 25 625 132 HOH HOH . 
I 3 HOH A 26 626 121 HOH HOH . 
J 3 HOH B 1 601 122 HOH HOH . 
J 3 HOH B 2 602 9 HOH HOH . 
J 3 HOH B 3 603 21 HOH HOH . 
J 3 HOH B 4 604 10 HOH HOH . 
J 3 HOH B 5 605 14 HOH HOH . 
J 3 HOH B 6 606 2 HOH HOH . 
J 3 HOH B 7 607 15 HOH HOH . 
J 3 HOH B 8 608 126 HOH HOH . 
J 3 HOH B 9 609 4 HOH HOH . 
J 3 HOH B 10 610 64 HOH HOH . 
J 3 HOH B 11 611 33 HOH HOH . 
J 3 HOH B 12 612 75 HOH HOH . 
J 3 HOH B 13 613 115 HOH HOH . 
J 3 HOH B 14 614 128 HOH HOH . 
J 3 HOH B 15 615 92 HOH HOH . 
J 3 HOH B 16 616 66 HOH HOH . 
J 3 HOH B 17 617 103 HOH HOH . 
J 3 HOH B 18 618 134 HOH HOH . 
J 3 HOH B 19 619 91 HOH HOH . 
J 3 HOH B 20 620 95 HOH HOH . 
J 3 HOH B 21 621 90 HOH HOH . 
J 3 HOH B 22 622 124 HOH HOH . 
J 3 HOH B 23 623 113 HOH HOH . 
J 3 HOH B 24 624 74 HOH HOH . 
J 3 HOH B 25 625 93 HOH HOH . 
J 3 HOH B 26 626 94 HOH HOH . 
J 3 HOH B 27 627 116 HOH HOH . 
J 3 HOH B 28 628 96 HOH HOH . 
J 3 HOH B 29 629 114 HOH HOH . 
J 3 HOH B 30 630 133 HOH HOH . 
K 3 HOH C 1 601 18 HOH HOH . 
K 3 HOH C 2 602 45 HOH HOH . 
K 3 HOH C 3 603 20 HOH HOH . 
K 3 HOH C 4 604 111 HOH HOH . 
K 3 HOH C 5 605 57 HOH HOH . 
K 3 HOH C 6 606 24 HOH HOH . 
K 3 HOH C 7 607 41 HOH HOH . 
K 3 HOH C 8 608 53 HOH HOH . 
K 3 HOH C 9 609 19 HOH HOH . 
K 3 HOH C 10 610 123 HOH HOH . 
K 3 HOH C 11 611 22 HOH HOH . 
K 3 HOH C 12 612 79 HOH HOH . 
K 3 HOH C 13 613 98 HOH HOH . 
K 3 HOH C 14 614 6 HOH HOH . 
K 3 HOH C 15 615 27 HOH HOH . 
K 3 HOH C 16 616 52 HOH HOH . 
K 3 HOH C 17 617 105 HOH HOH . 
K 3 HOH C 18 618 130 HOH HOH . 
K 3 HOH C 19 619 120 HOH HOH . 
K 3 HOH C 20 620 127 HOH HOH . 
K 3 HOH C 21 621 78 HOH HOH . 
K 3 HOH C 22 622 129 HOH HOH . 
K 3 HOH C 23 623 107 HOH HOH . 
K 3 HOH C 24 624 100 HOH HOH . 
K 3 HOH C 25 625 76 HOH HOH . 
K 3 HOH C 26 626 68 HOH HOH . 
K 3 HOH C 27 627 77 HOH HOH . 
L 3 HOH D 1 601 1 HOH HOH . 
L 3 HOH D 2 602 48 HOH HOH . 
L 3 HOH D 3 603 32 HOH HOH . 
L 3 HOH D 4 604 16 HOH HOH . 
L 3 HOH D 5 605 80 HOH HOH . 
L 3 HOH D 6 606 30 HOH HOH . 
L 3 HOH D 7 607 81 HOH HOH . 
L 3 HOH D 8 608 101 HOH HOH . 
L 3 HOH D 9 609 51 HOH HOH . 
L 3 HOH D 10 610 61 HOH HOH . 
L 3 HOH D 11 611 25 HOH HOH . 
L 3 HOH D 12 612 102 HOH HOH . 
L 3 HOH D 13 613 46 HOH HOH . 
L 3 HOH D 14 614 7 HOH HOH . 
L 3 HOH D 15 615 28 HOH HOH . 
L 3 HOH D 16 616 86 HOH HOH . 
L 3 HOH D 17 617 87 HOH HOH . 
L 3 HOH D 18 618 131 HOH HOH . 
L 3 HOH D 19 619 83 HOH HOH . 
L 3 HOH D 20 620 88 HOH HOH . 
L 3 HOH D 21 621 117 HOH HOH . 
L 3 HOH D 22 622 125 HOH HOH . 
L 3 HOH D 23 623 73 HOH HOH . 
L 3 HOH D 24 624 82 HOH HOH . 
L 3 HOH D 25 625 106 HOH HOH . 
L 3 HOH D 26 626 44 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 . . . H 2 1.233 39.345 20.639 1 42.28 ? PB GDP 500 D 1 
HETATM 2 O O1B GDP . . . H 2 -0.035 39.575 19.853 1 41.9 ? O1B GDP 500 D 1 
HETATM 3 O O2B GDP . . . H 2 1.089 38.093 21.471 1 43.91 ? O2B GDP 500 D 1 
HETATM 4 O O3B GDP . . . H 2 1.509 40.531 21.536 1 38.15 ? O3B GDP 500 D 1 
HETATM 5 O O3A GDP . . . H 2 2.429 39.145 19.588 1 43.26 ? O3A GDP 500 D 1 
HETATM 6 P PA GDP . . . H 2 3.761 40.04 19.676 1 44.68 ? PA GDP 500 D 1 
HETATM 7 O O1A GDP . . . H 2 3.513 41.459 19.217 1 44.13 ? O1A GDP 500 D 1 
HETATM 8 O O2A GDP . . . H 2 4.334 40.006 21.075 1 46.41 ? O2A GDP 500 D 1 
HETATM 9 O O5' GDP . . . H 2 4.709 39.268 18.635 1 44.51 ? O5' GDP 500 D 1 
HETATM 10 C C5' GDP . . . H 2 5.375 38.078 19.046 1 44.35 ? C5' GDP 500 D 1 
HETATM 11 C C4' GDP . . . H 2 6.439 37.733 18.019 1 42.12 ? C4' GDP 500 D 1 
HETATM 12 O O4' GDP . . . H 2 5.875 37.793 16.708 1 40.28 ? O4' GDP 500 D 1 
HETATM 13 C C3' GDP . . . H 2 7.578 38.737 18.074 1 43.82 ? C3' GDP 500 D 1 
HETATM 14 O O3' GDP . . . H 2 8.778 38.079 18.494 1 42.09 ? O3' GDP 500 D 1 
HETATM 15 C C2' GDP . . . H 2 7.724 39.274 16.663 1 46.23 ? C2' GDP 500 D 1 
HETATM 16 O O2' GDP . . . H 2 9.076 39.145 16.215 1 51 ? O2' GDP 500 D 1 
HETATM 17 C C1' GDP . . . H 2 6.796 38.419 15.812 1 43.44 ? C1' GDP 500 D 1 
HETATM 18 N N9 GDP . . . H 2 6.073 39.249 14.818 1 42.64 ? N9 GDP 500 D 1 
HETATM 19 C C8 GDP . . . H 2 5.136 40.181 15.08 1 40.41 ? C8 GDP 500 D 1 
HETATM 20 N N7 GDP . . . H 2 4.676 40.746 13.935 1 38.75 ? N7 GDP 500 D 1 
HETATM 21 C C5 GDP . . . H 2 5.325 40.161 12.912 1 39.92 ? C5 GDP 500 D 1 
HETATM 22 C C6 GDP . . . H 2 5.322 40.277 11.437 1 37.55 ? C6 GDP 500 D 1 
HETATM 23 O O6 GDP . . . H 2 4.575 41.094 10.859 1 38.3 ? O6 GDP 500 D 1 
HETATM 24 N N1 GDP . . . H 2 6.152 39.486 10.744 1 35.83 ? N1 GDP 500 D 1 
HETATM 25 C C2 GDP . . . H 2 6.973 38.598 11.336 1 37.04 ? C2 GDP 500 D 1 
HETATM 26 N N2 GDP . . . H 2 7.781 37.834 10.561 1 37.18 ? N2 GDP 500 D 1 
HETATM 27 N N3 GDP . . . H 2 7.026 38.438 12.681 1 41.51 ? N3 GDP 500 D 1 
HETATM 28 C C4 GDP . . . H 2 6.243 39.177 13.5 1 41.1 ? C4 GDP 500 D 1 
#
_model_server_stats.io_time_ms              72 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           214 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           28 
#