data_6PTA
#
_model_server_result.job_id            lygn4zvDiTlVV90MX9RCmg 
_model_server_result.datetime_utc      '2025-03-11 11:20:32' 
_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":"F","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 . . . F 2 6.116 35.435 32.19 1 33.32 ? PB GDP 500 B 1 
HETATM 2 O O1B GDP . . . F 2 6.151 34.91 30.769 1 35.58 ? O1B GDP 500 B 1 
HETATM 3 O O2B GDP . . . F 2 7.39 35.032 32.895 1 33.77 ? O2B GDP 500 B 1 
HETATM 4 O O3B GDP . . . F 2 5.987 36.941 32.198 1 30.6 ? O3B GDP 500 B 1 
HETATM 5 O O3A GDP . . . F 2 4.865 34.763 32.941 1 39.75 ? O3A GDP 500 B 1 
HETATM 6 P PA GDP . . . F 2 3.578 35.614 33.397 1 40.49 ? PA GDP 500 B 1 
HETATM 7 O O1A GDP . . . F 2 2.986 36.39 32.246 1 44.02 ? O1A GDP 500 B 1 
HETATM 8 O O2A GDP . . . F 2 3.889 36.521 34.563 1 41.34 ? O2A GDP 500 B 1 
HETATM 9 O O5' GDP . . . F 2 2.608 34.426 33.857 1 40.98 ? O5' GDP 500 B 1 
HETATM 10 C C5' GDP . . . F 2 2.203 33.442 32.911 1 39.84 ? C5' GDP 500 B 1 
HETATM 11 C C4' GDP . . . F 2 1.139 32.598 33.587 1 40.4 ? C4' GDP 500 B 1 
HETATM 12 O O4' GDP . . . F 2 1.685 31.975 34.754 1 37.47 ? O4' GDP 500 B 1 
HETATM 13 C C3' GDP . . . F 2 0.007 33.501 34.048 1 42.14 ? C3' GDP 500 B 1 
HETATM 14 O O3' GDP . . . F 2 -1.22 33.08 33.449 1 43.99 ? O3' GDP 500 B 1 
HETATM 15 C C2' GDP . . . F 2 -0.062 33.334 35.553 1 42.54 ? C2' GDP 500 B 1 
HETATM 16 O O2' GDP . . . F 2 -1.417 33.193 35.99 1 44.3 ? O2' GDP 500 B 1 
HETATM 17 C C1' GDP . . . F 2 0.746 32.076 35.827 1 38.39 ? C1' GDP 500 B 1 
HETATM 18 N N9 GDP . . . F 2 1.436 32.18 37.131 1 35.25 ? N9 GDP 500 B 1 
HETATM 19 C C8 GDP . . . F 2 2.34 33.11 37.486 1 35.26 ? C8 GDP 500 B 1 
HETATM 20 N N7 GDP . . . F 2 2.776 32.904 38.755 1 34.46 ? N7 GDP 500 B 1 
HETATM 21 C C5 GDP . . . F 2 2.145 31.814 39.227 1 33.93 ? C5 GDP 500 B 1 
HETATM 22 C C6 GDP . . . F 2 2.137 31.045 40.492 1 34.15 ? C6 GDP 500 B 1 
HETATM 23 O O6 GDP . . . F 2 2.862 31.391 41.447 1 35.32 ? O6 GDP 500 B 1 
HETATM 24 N N1 GDP . . . F 2 1.336 29.974 40.574 1 33.72 ? N1 GDP 500 B 1 
HETATM 25 C C2 GDP . . . F 2 0.551 29.585 39.549 1 34.83 ? C2 GDP 500 B 1 
HETATM 26 N N2 GDP . . . F 2 -0.236 28.493 39.697 1 37.08 ? N2 GDP 500 B 1 
HETATM 27 N N3 GDP . . . F 2 0.507 30.244 38.365 1 33.21 ? N3 GDP 500 B 1 
HETATM 28 C C4 GDP . . . F 2 1.264 31.343 38.152 1 34.54 ? C4 GDP 500 B 1 
#
_model_server_stats.io_time_ms              60 
_model_server_stats.parse_time_ms           93 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           1195 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           28 
#