data_6R4A
#
_model_server_result.job_id            PVjsMVnN9HvRRPGeQqx3ng 
_model_server_result.datetime_utc      '2024-11-25 15:33:15' 
_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          6r4a 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":501}' 
#
_entry.id    6R4A 
#
_exptl.entry_id    6R4A 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          2 
_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         120 
_cell.entry_id            6R4A 
_cell.length_a            81.37 
_cell.length_b            81.37 
_cell.length_c            175.959 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6R4A 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61 2 2' 
#
_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,I,J,K,L 
_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                      2 
_struct_asym.id                             B 
_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
covale ? covale1 A C THR 169 A THR 287 1_555 A N TPO 170 A TPO 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale2 A C TPO 170 A TPO 288 1_555 A N LEU 171 A LEU 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
metalc ? metalc1 A OD1 ASN 143 A ASN 261 1_555 E MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? 
metalc ? metalc2 A OD2 ASP 156 A ASP 274 1_555 E MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
metalc ? metalc3 A OD1 ASP 156 A ASP 274 1_555 F MG MG . A MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? 
metalc ? metalc4 B O3B ADP . A ADP 501 1_555 E MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
metalc ? metalc5 B O2A ADP . A ADP 501 1_555 E MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? 
metalc ? metalc6 B O1B ADP . A ADP 501 1_555 F MG MG . A MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? 
metalc ? metalc7 E MG MG . A MG 504 1_555 L O HOH . A HOH 658 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? 
metalc ? metalc8 E MG MG . A MG 504 1_555 L O HOH . A HOH 672 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? 
metalc ? metalc9 F MG MG . A MG 505 1_555 L O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? 
metalc ? metalc10 F MG MG . A MG 505 1_555 L O HOH . A HOH 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? 
metalc ? metalc11 F MG MG . A MG 505 1_555 L O HOH . A HOH 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? 
#
_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                     6R4A 
_atom_sites.fract_transf_matrix[1][1]    0.01229 
_atom_sites.fract_transf_matrix[1][2]    0.007095 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014191 
_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]    0.005683 
_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 ADP A 1 501 1392 ADP ADP . 
C 3 GOL A 1 502 1393 GOL GOL . 
D 3 GOL A 1 503 1394 GOL GOL . 
E 4 MG A 1 504 1395 MG MG . 
F 4 MG A 1 505 1396 MG MG . 
G 5 CL A 1 506 1397 CL CL . 
H 5 CL A 1 507 1398 CL CL . 
I 5 CL A 1 508 1399 CL CL . 
J 5 CL A 1 509 1400 CL CL . 
K 6 JRT A 1 510 1 JRT LIG . 
L 7 HOH A 1 601 72 HOH HOH . 
L 7 HOH A 2 602 6 HOH HOH . 
L 7 HOH A 3 603 101 HOH HOH . 
L 7 HOH A 4 604 41 HOH HOH . 
L 7 HOH A 5 605 117 HOH HOH . 
L 7 HOH A 6 606 77 HOH HOH . 
L 7 HOH A 7 607 13 HOH HOH . 
L 7 HOH A 8 608 46 HOH HOH . 
L 7 HOH A 9 609 118 HOH HOH . 
L 7 HOH A 10 610 96 HOH HOH . 
L 7 HOH A 11 611 55 HOH HOH . 
L 7 HOH A 12 612 83 HOH HOH . 
L 7 HOH A 13 613 78 HOH HOH . 
L 7 HOH A 14 614 40 HOH HOH . 
L 7 HOH A 15 615 7 HOH HOH . 
L 7 HOH A 16 616 58 HOH HOH . 
L 7 HOH A 17 617 70 HOH HOH . 
L 7 HOH A 18 618 9 HOH HOH . 
L 7 HOH A 19 619 123 HOH HOH . 
L 7 HOH A 20 620 18 HOH HOH . 
L 7 HOH A 21 621 64 HOH HOH . 
L 7 HOH A 22 622 22 HOH HOH . 
L 7 HOH A 23 623 37 HOH HOH . 
L 7 HOH A 24 624 39 HOH HOH . 
L 7 HOH A 25 625 29 HOH HOH . 
L 7 HOH A 26 626 60 HOH HOH . 
L 7 HOH A 27 627 53 HOH HOH . 
L 7 HOH A 28 628 2 HOH HOH . 
L 7 HOH A 29 629 80 HOH HOH . 
L 7 HOH A 30 630 27 HOH HOH . 
L 7 HOH A 31 631 92 HOH HOH . 
L 7 HOH A 32 632 23 HOH HOH . 
L 7 HOH A 33 633 113 HOH HOH . 
L 7 HOH A 34 634 52 HOH HOH . 
L 7 HOH A 35 635 16 HOH HOH . 
L 7 HOH A 36 636 44 HOH HOH . 
L 7 HOH A 37 637 63 HOH HOH . 
L 7 HOH A 38 638 12 HOH HOH . 
L 7 HOH A 39 639 95 HOH HOH . 
L 7 HOH A 40 640 57 HOH HOH . 
L 7 HOH A 41 641 36 HOH HOH . 
L 7 HOH A 42 642 79 HOH HOH . 
L 7 HOH A 43 643 42 HOH HOH . 
L 7 HOH A 44 644 15 HOH HOH . 
L 7 HOH A 45 645 45 HOH HOH . 
L 7 HOH A 46 646 65 HOH HOH . 
L 7 HOH A 47 647 3 HOH HOH . 
L 7 HOH A 48 648 76 HOH HOH . 
L 7 HOH A 49 649 73 HOH HOH . 
L 7 HOH A 50 650 90 HOH HOH . 
L 7 HOH A 51 651 1 HOH HOH . 
L 7 HOH A 52 652 86 HOH HOH . 
L 7 HOH A 53 653 30 HOH HOH . 
L 7 HOH A 54 654 47 HOH HOH . 
L 7 HOH A 55 655 115 HOH HOH . 
L 7 HOH A 56 656 4 HOH HOH . 
L 7 HOH A 57 657 28 HOH HOH . 
L 7 HOH A 58 658 32 HOH HOH . 
L 7 HOH A 59 659 21 HOH HOH . 
L 7 HOH A 60 660 17 HOH HOH . 
L 7 HOH A 61 661 75 HOH HOH . 
L 7 HOH A 62 662 99 HOH HOH . 
L 7 HOH A 63 663 68 HOH HOH . 
L 7 HOH A 64 664 26 HOH HOH . 
L 7 HOH A 65 665 5 HOH HOH . 
L 7 HOH A 66 666 66 HOH HOH . 
L 7 HOH A 67 667 33 HOH HOH . 
L 7 HOH A 68 668 88 HOH HOH . 
L 7 HOH A 69 669 85 HOH HOH . 
L 7 HOH A 70 670 81 HOH HOH . 
L 7 HOH A 71 671 25 HOH HOH . 
L 7 HOH A 72 672 31 HOH HOH . 
L 7 HOH A 73 673 38 HOH HOH . 
L 7 HOH A 74 674 10 HOH HOH . 
L 7 HOH A 75 675 108 HOH HOH . 
L 7 HOH A 76 676 11 HOH HOH . 
L 7 HOH A 77 677 69 HOH HOH . 
L 7 HOH A 78 678 24 HOH HOH . 
L 7 HOH A 79 679 97 HOH HOH . 
L 7 HOH A 80 680 82 HOH HOH . 
L 7 HOH A 81 681 125 HOH HOH . 
L 7 HOH A 82 682 8 HOH HOH . 
L 7 HOH A 83 683 114 HOH HOH . 
L 7 HOH A 84 684 124 HOH HOH . 
L 7 HOH A 85 685 98 HOH HOH . 
L 7 HOH A 86 686 87 HOH HOH . 
L 7 HOH A 87 687 62 HOH HOH . 
L 7 HOH A 88 688 94 HOH HOH . 
L 7 HOH A 89 689 61 HOH HOH . 
L 7 HOH A 90 690 91 HOH HOH . 
L 7 HOH A 91 691 93 HOH HOH . 
L 7 HOH A 92 692 35 HOH HOH . 
L 7 HOH A 93 693 20 HOH HOH . 
L 7 HOH A 94 694 43 HOH HOH . 
L 7 HOH A 95 695 34 HOH HOH . 
L 7 HOH A 96 696 106 HOH HOH . 
L 7 HOH A 97 697 19 HOH HOH . 
L 7 HOH A 98 698 50 HOH HOH . 
L 7 HOH A 99 699 51 HOH HOH . 
L 7 HOH A 100 700 104 HOH HOH . 
L 7 HOH A 101 701 54 HOH HOH . 
L 7 HOH A 102 702 111 HOH HOH . 
L 7 HOH A 103 703 49 HOH HOH . 
L 7 HOH A 104 704 56 HOH HOH . 
L 7 HOH A 105 705 109 HOH HOH . 
L 7 HOH A 106 706 14 HOH HOH . 
L 7 HOH A 107 707 71 HOH HOH . 
L 7 HOH A 108 708 110 HOH HOH . 
L 7 HOH A 109 709 105 HOH HOH . 
L 7 HOH A 110 710 84 HOH HOH . 
L 7 HOH A 111 711 116 HOH HOH . 
L 7 HOH A 112 712 103 HOH HOH . 
L 7 HOH A 113 713 48 HOH HOH . 
L 7 HOH A 114 714 112 HOH HOH . 
L 7 HOH A 115 715 102 HOH HOH . 
L 7 HOH A 116 716 67 HOH HOH . 
L 7 HOH A 117 717 122 HOH HOH . 
L 7 HOH A 118 718 127 HOH HOH . 
L 7 HOH A 119 719 100 HOH HOH . 
L 7 HOH A 120 720 126 HOH HOH . 
L 7 HOH A 121 721 107 HOH HOH . 
L 7 HOH A 122 722 59 HOH HOH . 
L 7 HOH A 123 723 119 HOH HOH . 
L 7 HOH A 124 724 89 HOH HOH . 
L 7 HOH A 125 725 121 HOH HOH . 
L 7 HOH A 126 726 74 HOH HOH . 
L 7 HOH A 127 727 120 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 . . . B 2 -12.249 23.742 -6.259 1 29.13 ? PB ADP 501 A 1 
HETATM 2 O O1B ADP . . . B 2 -12.868 23.343 -7.577 1 29.44 ? O1B ADP 501 A 1 
HETATM 3 O O2B ADP . . . B 2 -11.703 22.527 -5.53 1 33.05 ? O2B ADP 501 A 1 
HETATM 4 O O3B ADP . . . B 2 -13.01 24.727 -5.388 1 28.91 ? O3B ADP 501 A 1 
HETATM 5 P PA ADP . . . B 2 -10.776 26.069 -7.221 1 27.41 ? PA ADP 501 A 1 
HETATM 6 O O1A ADP . . . B 2 -10.564 26.148 -8.712 1 34.41 ? O1A ADP 501 A 1 
HETATM 7 O O2A ADP . . . B 2 -11.882 26.9 -6.62 1 30.17 ? O2A ADP 501 A 1 
HETATM 8 O O3A ADP . . . B 2 -10.891 24.552 -6.689 1 28.39 ? O3A ADP 501 A 1 
HETATM 9 O O5' ADP . . . B 2 -9.375 26.58 -6.541 1 28.63 ? O5' ADP 501 A 1 
HETATM 10 C C5' ADP . . . B 2 -9.197 26.512 -5.122 1 27.78 ? C5' ADP 501 A 1 
HETATM 11 C C4' ADP . . . B 2 -8.447 27.73 -4.577 1 26.17 ? C4' ADP 501 A 1 
HETATM 12 O O4' ADP . . . B 2 -7.149 27.869 -5.185 1 26.97 ? O4' ADP 501 A 1 
HETATM 13 C C3' ADP . . . B 2 -9.165 29.036 -4.862 1 31.57 ? C3' ADP 501 A 1 
HETATM 14 O O3' ADP . . . B 2 -10.129 29.342 -3.849 1 29.97 ? O3' ADP 501 A 1 
HETATM 15 C C2' ADP . . . B 2 -8.019 30.022 -4.824 1 30.7 ? C2' ADP 501 A 1 
HETATM 16 O O2' ADP . . . B 2 -7.702 30.23 -3.441 1 29.48 ? O2' ADP 501 A 1 
HETATM 17 C C1' ADP . . . B 2 -6.874 29.25 -5.452 1 23.3 ? C1' ADP 501 A 1 
HETATM 18 N N9 ADP . . . B 2 -6.812 29.451 -6.924 1 23.72 ? N9 ADP 501 A 1 
HETATM 19 C C8 ADP . . . B 2 -7.488 28.704 -7.825 1 30.26 ? C8 ADP 501 A 1 
HETATM 20 N N7 ADP . . . B 2 -7.231 29.099 -9.096 1 26.33 ? N7 ADP 501 A 1 
HETATM 21 C C5 ADP . . . B 2 -6.35 30.124 -9.014 1 27.53 ? C5 ADP 501 A 1 
HETATM 22 C C6 ADP . . . B 2 -5.667 30.991 -9.994 1 25.1 ? C6 ADP 501 A 1 
HETATM 23 N N6 ADP . . . B 2 -5.886 30.815 -11.321 1 27.26 ? N6 ADP 501 A 1 
HETATM 24 N N1 ADP . . . B 2 -4.835 31.947 -9.512 1 25.78 ? N1 ADP 501 A 1 
HETATM 25 C C2 ADP . . . B 2 -4.624 32.104 -8.184 1 32.19 ? C2 ADP 501 A 1 
HETATM 26 N N3 ADP . . . B 2 -5.206 31.339 -7.23 1 27.7 ? N3 ADP 501 A 1 
HETATM 27 C C4 ADP . . . B 2 -6.077 30.349 -7.585 1 24 ? C4 ADP 501 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           26 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           279 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           27 
#