data_6YXT
#
_model_server_result.job_id            '_bWX_QZvW71_eZg9o6VhAQ' 
_model_server_result.datetime_utc      '2025-01-11 15:41:30' 
_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          6yxt 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":503}' 
#
_entry.id    6YXT 
#
_exptl.entry_id    6YXT 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_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            6YXT 
_cell.length_a            66.45 
_cell.length_b            68 
_cell.length_c            105.11 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YXT 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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,G,H 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 OD1 ASN 235 A ASN 293 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? 
metalc ? metalc2 A OD1 ASP 247 A ASP 305 1_555 B MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? 
metalc ? metalc3 A OD2 ASP 247 A ASP 305 1_555 B MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
metalc ? metalc4 A OD2 ASP 247 A ASP 305 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? 
metalc ? metalc5 A OE2 GLU 249 A GLU 307 1_555 B MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? 
metalc ? metalc6 B MG MG . A MG 501 1_555 D O2B ADP . A ADP 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? 
metalc ? metalc7 B MG MG . A MG 501 1_555 D O3B ADP . A ADP 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.926 ? 
metalc ? metalc8 B MG MG . A MG 501 1_555 H O HOH . A HOH 613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? 
metalc ? metalc9 B MG MG . A MG 501 1_555 H O HOH . A HOH 677 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? 
metalc ? metalc10 C MG MG . A MG 502 1_555 D O2A ADP . A ADP 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? 
metalc ? metalc11 C MG MG . A MG 502 1_555 D O3B ADP . A ADP 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? 
metalc ? metalc12 C MG MG . A MG 502 1_555 H O HOH . A HOH 614 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
metalc ? metalc13 C MG MG . A MG 502 1_555 H O HOH . A HOH 642 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
#
_chem_comp.formula           'C10 H15 N5 O10 P2' 
_chem_comp.formula_weight    427.201 
_chem_comp.id                ADP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "ADENOSINE-5'-DIPHOSPHATE" 
_chem_comp.type              non-polymer 
_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 ADP doub 1 n n 
PB O2B ADP sing 2 n n 
PB O3B ADP sing 3 n n 
PB O3A ADP sing 4 n n 
O2B HOB2 ADP sing 5 n n 
O3B HOB3 ADP sing 6 n n 
PA O1A ADP doub 7 n n 
PA O2A ADP sing 8 n n 
PA O3A ADP sing 9 n n 
PA O5' ADP sing 10 n n 
O2A HOA2 ADP sing 11 n n 
O5' C5' ADP sing 12 n n 
C5' C4' ADP sing 13 n n 
C5' "H5'1" ADP sing 14 n n 
C5' "H5'2" ADP sing 15 n n 
C4' O4' ADP sing 16 n n 
C4' C3' ADP sing 17 n n 
C4' H4' ADP sing 18 n n 
O4' C1' ADP sing 19 n n 
C3' O3' ADP sing 20 n n 
C3' C2' ADP sing 21 n n 
C3' H3' ADP sing 22 n n 
O3' HO3' ADP sing 23 n n 
C2' O2' ADP sing 24 n n 
C2' C1' ADP sing 25 n n 
C2' H2' ADP sing 26 n n 
O2' HO2' ADP sing 27 n n 
C1' N9 ADP sing 28 n n 
C1' H1' ADP sing 29 n n 
N9 C8 ADP sing 30 n y 
N9 C4 ADP sing 31 n y 
C8 N7 ADP doub 32 n y 
C8 H8 ADP sing 33 n n 
N7 C5 ADP sing 34 n y 
C5 C6 ADP sing 35 n y 
C5 C4 ADP doub 36 n y 
C6 N6 ADP sing 37 n n 
C6 N1 ADP doub 38 n y 
N6 HN61 ADP sing 39 n n 
N6 HN62 ADP sing 40 n n 
N1 C2 ADP sing 41 n y 
C2 N3 ADP doub 42 n y 
C2 H2 ADP sing 43 n n 
N3 C4 ADP sing 44 n y 
#
_atom_sites.entry_id                     6YXT 
_atom_sites.fract_transf_matrix[1][1]    0.015049 
_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]    0.014706 
_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]    0.009514 
_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
B 2 MG A 1 501 1 MG MG . 
C 2 MG A 1 502 2 MG MG . 
D 3 ADP A 1 503 1 ADP ADP . 
E 4 EDO A 1 504 2 EDO EDO . 
F 4 EDO A 1 505 3 EDO EDO . 
G 4 EDO A 1 506 9 EDO EDO . 
H 5 HOH A 1 601 159 HOH HOH . 
H 5 HOH A 2 602 160 HOH HOH . 
H 5 HOH A 3 603 62 HOH HOH . 
H 5 HOH A 4 604 127 HOH HOH . 
H 5 HOH A 5 605 157 HOH HOH . 
H 5 HOH A 6 606 68 HOH HOH . 
H 5 HOH A 7 607 95 HOH HOH . 
H 5 HOH A 8 608 138 HOH HOH . 
H 5 HOH A 9 609 81 HOH HOH . 
H 5 HOH A 10 610 38 HOH HOH . 
H 5 HOH A 11 611 17 HOH HOH . 
H 5 HOH A 12 612 7 HOH HOH . 
H 5 HOH A 13 613 45 HOH HOH . 
H 5 HOH A 14 614 107 HOH HOH . 
H 5 HOH A 15 615 97 HOH HOH . 
H 5 HOH A 16 616 56 HOH HOH . 
H 5 HOH A 17 617 149 HOH HOH . 
H 5 HOH A 18 618 29 HOH HOH . 
H 5 HOH A 19 619 101 HOH HOH . 
H 5 HOH A 20 620 96 HOH HOH . 
H 5 HOH A 21 621 158 HOH HOH . 
H 5 HOH A 22 622 141 HOH HOH . 
H 5 HOH A 23 623 99 HOH HOH . 
H 5 HOH A 24 624 4 HOH HOH . 
H 5 HOH A 25 625 93 HOH HOH . 
H 5 HOH A 26 626 36 HOH HOH . 
H 5 HOH A 27 627 19 HOH HOH . 
H 5 HOH A 28 628 103 HOH HOH . 
H 5 HOH A 29 629 40 HOH HOH . 
H 5 HOH A 30 630 102 HOH HOH . 
H 5 HOH A 31 631 142 HOH HOH . 
H 5 HOH A 32 632 24 HOH HOH . 
H 5 HOH A 33 633 11 HOH HOH . 
H 5 HOH A 34 634 44 HOH HOH . 
H 5 HOH A 35 635 43 HOH HOH . 
H 5 HOH A 36 636 23 HOH HOH . 
H 5 HOH A 37 637 113 HOH HOH . 
H 5 HOH A 38 638 79 HOH HOH . 
H 5 HOH A 39 639 144 HOH HOH . 
H 5 HOH A 40 640 18 HOH HOH . 
H 5 HOH A 41 641 134 HOH HOH . 
H 5 HOH A 42 642 106 HOH HOH . 
H 5 HOH A 43 643 50 HOH HOH . 
H 5 HOH A 44 644 1 HOH HOH . 
H 5 HOH A 45 645 47 HOH HOH . 
H 5 HOH A 46 646 33 HOH HOH . 
H 5 HOH A 47 647 21 HOH HOH . 
H 5 HOH A 48 648 71 HOH HOH . 
H 5 HOH A 49 649 94 HOH HOH . 
H 5 HOH A 50 650 98 HOH HOH . 
H 5 HOH A 51 651 121 HOH HOH . 
H 5 HOH A 52 652 64 HOH HOH . 
H 5 HOH A 53 653 155 HOH HOH . 
H 5 HOH A 54 654 37 HOH HOH . 
H 5 HOH A 55 655 90 HOH HOH . 
H 5 HOH A 56 656 119 HOH HOH . 
H 5 HOH A 57 657 22 HOH HOH . 
H 5 HOH A 58 658 139 HOH HOH . 
H 5 HOH A 59 659 8 HOH HOH . 
H 5 HOH A 60 660 74 HOH HOH . 
H 5 HOH A 61 661 140 HOH HOH . 
H 5 HOH A 62 662 49 HOH HOH . 
H 5 HOH A 63 663 48 HOH HOH . 
H 5 HOH A 64 664 109 HOH HOH . 
H 5 HOH A 65 665 137 HOH HOH . 
H 5 HOH A 66 666 154 HOH HOH . 
H 5 HOH A 67 667 77 HOH HOH . 
H 5 HOH A 68 668 153 HOH HOH . 
H 5 HOH A 69 669 42 HOH HOH . 
H 5 HOH A 70 670 135 HOH HOH . 
H 5 HOH A 71 671 34 HOH HOH . 
H 5 HOH A 72 672 80 HOH HOH . 
H 5 HOH A 73 673 30 HOH HOH . 
H 5 HOH A 74 674 78 HOH HOH . 
H 5 HOH A 75 675 120 HOH HOH . 
H 5 HOH A 76 676 41 HOH HOH . 
H 5 HOH A 77 677 46 HOH HOH . 
H 5 HOH A 78 678 70 HOH HOH . 
H 5 HOH A 79 679 87 HOH HOH . 
H 5 HOH A 80 680 32 HOH HOH . 
H 5 HOH A 81 681 91 HOH HOH . 
H 5 HOH A 82 682 3 HOH HOH . 
H 5 HOH A 83 683 26 HOH HOH . 
H 5 HOH A 84 684 152 HOH HOH . 
H 5 HOH A 85 685 60 HOH HOH . 
H 5 HOH A 86 686 9 HOH HOH . 
H 5 HOH A 87 687 27 HOH HOH . 
H 5 HOH A 88 688 31 HOH HOH . 
H 5 HOH A 89 689 16 HOH HOH . 
H 5 HOH A 90 690 14 HOH HOH . 
H 5 HOH A 91 691 114 HOH HOH . 
H 5 HOH A 92 692 28 HOH HOH . 
H 5 HOH A 93 693 25 HOH HOH . 
H 5 HOH A 94 694 65 HOH HOH . 
H 5 HOH A 95 695 156 HOH HOH . 
H 5 HOH A 96 696 115 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 ADP . . . D 3 -11.298 -16.702 7.21 1 48.77 ? PB ADP 503 A 1 
HETATM 2 O O1B ADP . . . D 3 -10.26 -17.796 7.182 1 66.53 ? O1B ADP 503 A 1 
HETATM 3 O O2B ADP . . . D 3 -12.511 -17.041 8.042 1 71.03 ? O2B ADP 503 A 1 
HETATM 4 O O3B ADP . . . D 3 -10.727 -15.341 7.519 1 50.09 ? O3B ADP 503 A 1 
HETATM 5 P PA ADP . . . D 3 -11.808 -15.464 4.637 1 45.91 ? PA ADP 503 A 1 
HETATM 6 O O1A ADP . . . D 3 -13.169 -15.321 3.999 1 46.22 ? O1A ADP 503 A 1 
HETATM 7 O O2A ADP . . . D 3 -11.116 -14.261 5.228 1 53.71 ? O2A ADP 503 A 1 
HETATM 8 O O3A ADP . . . D 3 -11.883 -16.68 5.702 1 47.11 ? O3A ADP 503 A 1 
HETATM 9 O O5' ADP . . . D 3 -10.795 -16.062 3.539 1 46.72 ? O5' ADP 503 A 1 
HETATM 10 C C5' ADP . . . D 3 -9.392 -16.013 3.789 1 47.56 ? C5' ADP 503 A 1 
HETATM 11 C C4' ADP . . . D 3 -8.614 -15.822 2.493 1 46.85 ? C4' ADP 503 A 1 
HETATM 12 O O4' ADP . . . D 3 -9.344 -16.335 1.377 1 47.99 ? O4' ADP 503 A 1 
HETATM 13 C C3' ADP . . . D 3 -8.361 -14.351 2.214 1 42.31 ? C3' ADP 503 A 1 
HETATM 14 O O3' ADP . . . D 3 -7.027 -13.993 2.588 1 59.16 ? O3' ADP 503 A 1 
HETATM 15 C C2' ADP . . . D 3 -8.559 -14.186 0.721 1 42.94 ? C2' ADP 503 A 1 
HETATM 16 O O2' ADP . . . D 3 -7.289 -14.014 0.085 1 52.77 ? O2' ADP 503 A 1 
HETATM 17 C C1' ADP . . . D 3 -9.203 -15.477 0.242 1 35.81 ? C1' ADP 503 A 1 
HETATM 18 N N9 ADP . . . D 3 -10.548 -15.172 -0.305 1 53.26 ? N9 ADP 503 A 1 
HETATM 19 C C8 ADP . . . D 3 -11.703 -15.255 0.382 1 41.68 ? C8 ADP 503 A 1 
HETATM 20 N N7 ADP . . . D 3 -12.761 -14.911 -0.394 1 44.76 ? N7 ADP 503 A 1 
HETATM 21 C C5 ADP . . . D 3 -12.284 -14.598 -1.612 1 45.96 ? C5 ADP 503 A 1 
HETATM 22 C C6 ADP . . . D 3 -12.863 -14.152 -2.901 1 49.06 ? C6 ADP 503 A 1 
HETATM 23 N N6 ADP . . . D 3 -14.198 -13.969 -3.042 1 46.11 ? N6 ADP 503 A 1 
HETATM 24 N N1 ADP . . . D 3 -12.014 -13.935 -3.93 1 47.57 ? N1 ADP 503 A 1 
HETATM 25 C C2 ADP . . . D 3 -10.686 -14.114 -3.8 1 48.38 ? C2 ADP 503 A 1 
HETATM 26 N N3 ADP . . . D 3 -10.093 -14.516 -2.661 1 45.91 ? N3 ADP 503 A 1 
HETATM 27 C C4 ADP . . . D 3 -10.824 -14.772 -1.55 1 47 ? C4 ADP 503 A 1 
#
_model_server_stats.io_time_ms              91 
_model_server_stats.parse_time_ms           53 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           965 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#