data_4KV9
#
_model_server_result.job_id            298KBfqyyEVXbr1obCfz7Q 
_model_server_result.datetime_utc      '2025-07-10 18:34:59' 
_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          4kv9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":500}' 
#
_entry.id    4KV9 
#
_exptl.entry_id    4KV9 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          112.17 
_cell.angle_gamma         90 
_cell.entry_id            4KV9 
_cell.length_a            160.9 
_cell.length_b            45.05 
_cell.length_c            95.49 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4KV9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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 C N N 
? 2 D 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                     4KV9 
_atom_sites.fract_transf_matrix[1][1]    0.006215 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002533 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.022198 
_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]    0.011308 
_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
C 2 GDP A 1 500 500 GDP GDP . 
D 2 GDP B 1 500 500 GDP GDP . 
E 3 HOH A 1 601 2 HOH HOH . 
E 3 HOH A 2 602 3 HOH HOH . 
E 3 HOH A 3 603 7 HOH HOH . 
E 3 HOH A 4 604 9 HOH HOH . 
E 3 HOH A 5 605 10 HOH HOH . 
E 3 HOH A 6 606 12 HOH HOH . 
E 3 HOH A 7 607 14 HOH HOH . 
E 3 HOH A 8 608 20 HOH HOH . 
E 3 HOH A 9 609 21 HOH HOH . 
E 3 HOH A 10 610 22 HOH HOH . 
E 3 HOH A 11 611 23 HOH HOH . 
E 3 HOH A 12 612 24 HOH HOH . 
E 3 HOH A 13 613 26 HOH HOH . 
E 3 HOH A 14 614 28 HOH HOH . 
E 3 HOH A 15 615 32 HOH HOH . 
E 3 HOH A 16 616 36 HOH HOH . 
E 3 HOH A 17 617 37 HOH HOH . 
E 3 HOH A 18 618 39 HOH HOH . 
E 3 HOH A 19 619 40 HOH HOH . 
E 3 HOH A 20 620 41 HOH HOH . 
E 3 HOH A 21 621 44 HOH HOH . 
E 3 HOH A 22 622 46 HOH HOH . 
E 3 HOH A 23 623 47 HOH HOH . 
E 3 HOH A 24 624 49 HOH HOH . 
E 3 HOH A 25 625 50 HOH HOH . 
E 3 HOH A 26 626 55 HOH HOH . 
E 3 HOH A 27 627 56 HOH HOH . 
E 3 HOH A 28 628 58 HOH HOH . 
E 3 HOH A 29 629 59 HOH HOH . 
E 3 HOH A 30 630 62 HOH HOH . 
E 3 HOH A 31 631 67 HOH HOH . 
E 3 HOH A 32 632 68 HOH HOH . 
E 3 HOH A 33 633 70 HOH HOH . 
E 3 HOH A 34 634 71 HOH HOH . 
E 3 HOH A 35 635 76 HOH HOH . 
E 3 HOH A 36 636 77 HOH HOH . 
E 3 HOH A 37 637 78 HOH HOH . 
E 3 HOH A 38 638 79 HOH HOH . 
E 3 HOH A 39 639 80 HOH HOH . 
E 3 HOH A 40 640 81 HOH HOH . 
E 3 HOH A 41 641 82 HOH HOH . 
E 3 HOH A 42 642 85 HOH HOH . 
E 3 HOH A 43 643 86 HOH HOH . 
E 3 HOH A 44 644 89 HOH HOH . 
E 3 HOH A 45 645 90 HOH HOH . 
E 3 HOH A 46 646 92 HOH HOH . 
E 3 HOH A 47 647 95 HOH HOH . 
E 3 HOH A 48 648 96 HOH HOH . 
E 3 HOH A 49 649 97 HOH HOH . 
E 3 HOH A 50 650 98 HOH HOH . 
E 3 HOH A 51 651 99 HOH HOH . 
E 3 HOH A 52 652 101 HOH HOH . 
E 3 HOH A 53 653 102 HOH HOH . 
E 3 HOH A 54 654 104 HOH HOH . 
E 3 HOH A 55 655 106 HOH HOH . 
E 3 HOH A 56 656 107 HOH HOH . 
E 3 HOH A 57 657 108 HOH HOH . 
E 3 HOH A 58 658 110 HOH HOH . 
E 3 HOH A 59 659 112 HOH HOH . 
E 3 HOH A 60 660 115 HOH HOH . 
E 3 HOH A 61 661 117 HOH HOH . 
E 3 HOH A 62 662 118 HOH HOH . 
E 3 HOH A 63 663 119 HOH HOH . 
E 3 HOH A 64 664 122 HOH HOH . 
E 3 HOH A 65 665 123 HOH HOH . 
E 3 HOH A 66 666 124 HOH HOH . 
E 3 HOH A 67 667 127 HOH HOH . 
E 3 HOH A 68 668 129 HOH HOH . 
E 3 HOH A 69 669 131 HOH HOH . 
E 3 HOH A 70 670 132 HOH HOH . 
F 3 HOH B 1 601 73 HOH HOH . 
F 3 HOH B 2 602 111 HOH HOH . 
F 3 HOH B 3 603 1 HOH HOH . 
F 3 HOH B 4 604 4 HOH HOH . 
F 3 HOH B 5 605 5 HOH HOH . 
F 3 HOH B 6 606 6 HOH HOH . 
F 3 HOH B 7 607 8 HOH HOH . 
F 3 HOH B 8 608 11 HOH HOH . 
F 3 HOH B 9 609 13 HOH HOH . 
F 3 HOH B 10 610 15 HOH HOH . 
F 3 HOH B 11 611 16 HOH HOH . 
F 3 HOH B 12 612 17 HOH HOH . 
F 3 HOH B 13 613 18 HOH HOH . 
F 3 HOH B 14 614 19 HOH HOH . 
F 3 HOH B 15 615 25 HOH HOH . 
F 3 HOH B 16 616 27 HOH HOH . 
F 3 HOH B 17 617 29 HOH HOH . 
F 3 HOH B 18 618 30 HOH HOH . 
F 3 HOH B 19 619 31 HOH HOH . 
F 3 HOH B 20 620 33 HOH HOH . 
F 3 HOH B 21 621 34 HOH HOH . 
F 3 HOH B 22 622 35 HOH HOH . 
F 3 HOH B 23 623 38 HOH HOH . 
F 3 HOH B 24 624 43 HOH HOH . 
F 3 HOH B 25 625 45 HOH HOH . 
F 3 HOH B 26 626 48 HOH HOH . 
F 3 HOH B 27 627 51 HOH HOH . 
F 3 HOH B 28 628 52 HOH HOH . 
F 3 HOH B 29 629 53 HOH HOH . 
F 3 HOH B 30 630 54 HOH HOH . 
F 3 HOH B 31 631 57 HOH HOH . 
F 3 HOH B 32 632 60 HOH HOH . 
F 3 HOH B 33 633 61 HOH HOH . 
F 3 HOH B 34 634 63 HOH HOH . 
F 3 HOH B 35 635 64 HOH HOH . 
F 3 HOH B 36 636 65 HOH HOH . 
F 3 HOH B 37 637 66 HOH HOH . 
F 3 HOH B 38 638 69 HOH HOH . 
F 3 HOH B 39 639 72 HOH HOH . 
F 3 HOH B 40 640 74 HOH HOH . 
F 3 HOH B 41 641 75 HOH HOH . 
F 3 HOH B 42 642 84 HOH HOH . 
F 3 HOH B 43 643 87 HOH HOH . 
F 3 HOH B 44 644 88 HOH HOH . 
F 3 HOH B 45 645 91 HOH HOH . 
F 3 HOH B 46 646 93 HOH HOH . 
F 3 HOH B 47 647 100 HOH HOH . 
F 3 HOH B 48 648 103 HOH HOH . 
F 3 HOH B 49 649 105 HOH HOH . 
F 3 HOH B 50 650 109 HOH HOH . 
F 3 HOH B 51 651 113 HOH HOH . 
F 3 HOH B 52 652 114 HOH HOH . 
F 3 HOH B 53 653 116 HOH HOH . 
F 3 HOH B 54 654 120 HOH HOH . 
F 3 HOH B 55 655 121 HOH HOH . 
F 3 HOH B 56 656 125 HOH HOH . 
F 3 HOH B 57 657 126 HOH HOH . 
F 3 HOH B 58 658 128 HOH HOH . 
F 3 HOH B 59 659 130 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 . . . D 2 8.876 0.327 26.594 1 39.81 ? PB GDP 500 B 1 
HETATM 2 O O1B GDP . . . D 2 9.996 1.264 26.939 1 39.56 ? O1B GDP 500 B 1 
HETATM 3 O O2B GDP . . . D 2 7.809 1.059 25.82 1 46.32 ? O2B GDP 500 B 1 
HETATM 4 O O3B GDP . . . D 2 9.345 -0.855 25.778 1 31.47 ? O3B GDP 500 B 1 
HETATM 5 O O3A GDP . . . D 2 8.216 -0.381 27.884 1 39.63 ? O3A GDP 500 B 1 
HETATM 6 P PA GDP . . . D 2 8.378 0.064 29.422 1 42.4 ? PA GDP 500 B 1 
HETATM 7 O O1A GDP . . . D 2 9.787 -0.14 29.944 1 42.56 ? O1A GDP 500 B 1 
HETATM 8 O O2A GDP . . . D 2 7.903 1.487 29.487 1 37.79 ? O2A GDP 500 B 1 
HETATM 9 O O5' GDP . . . D 2 7.449 -1.034 30.1 1 41.96 ? O5' GDP 500 B 1 
HETATM 10 C C5' GDP . . . D 2 6.061 -1.09 29.767 1 39.38 ? C5' GDP 500 B 1 
HETATM 11 C C4' GDP . . . D 2 5.296 -1.832 30.845 1 36.6 ? C4' GDP 500 B 1 
HETATM 12 O O4' GDP . . . D 2 5.712 -3.2 30.985 1 41.1 ? O4' GDP 500 B 1 
HETATM 13 C C3' GDP . . . D 2 5.442 -1.182 32.2 1 43.18 ? C3' GDP 500 B 1 
HETATM 14 O O3' GDP . . . D 2 4.183 -1.38 32.854 1 45.57 ? O3' GDP 500 B 1 
HETATM 15 C C2' GDP . . . D 2 6.428 -2.089 32.877 1 39.88 ? C2' GDP 500 B 1 
HETATM 16 O O2' GDP . . . D 2 6.241 -2.068 34.283 1 42.77 ? O2' GDP 500 B 1 
HETATM 17 C C1' GDP . . . D 2 6.056 -3.448 32.346 1 37.73 ? C1' GDP 500 B 1 
HETATM 18 N N9 GDP . . . D 2 7.237 -4.296 32.361 1 34.44 ? N9 GDP 500 B 1 
HETATM 19 C C8 GDP . . . D 2 8.508 -3.86 32.14 1 33.89 ? C8 GDP 500 B 1 
HETATM 20 N N7 GDP . . . D 2 9.36 -4.908 32.187 1 33.96 ? N7 GDP 500 B 1 
HETATM 21 C C5 GDP . . . D 2 8.653 -6.02 32.437 1 30.59 ? C5 GDP 500 B 1 
HETATM 22 C C6 GDP . . . D 2 8.955 -7.451 32.593 1 38.77 ? C6 GDP 500 B 1 
HETATM 23 O O6 GDP . . . D 2 10.13 -7.871 32.525 1 37.39 ? O6 GDP 500 B 1 
HETATM 24 N N1 GDP . . . D 2 7.935 -8.28 32.847 1 38.48 ? N1 GDP 500 B 1 
HETATM 25 C C2 GDP . . . D 2 6.666 -7.855 32.904 1 33.57 ? C2 GDP 500 B 1 
HETATM 26 N N2 GDP . . . D 2 5.69 -8.768 33.14 1 32.51 ? N2 GDP 500 B 1 
HETATM 27 N N3 GDP . . . D 2 6.32 -6.561 32.766 1 32.75 ? N3 GDP 500 B 1 
HETATM 28 C C4 GDP . . . D 2 7.249 -5.617 32.535 1 33.64 ? C4 GDP 500 B 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           273 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           28 
#