data_8VMF
#
_model_server_result.job_id            v60-NWV_q56MMKBZBAu7Bw 
_model_server_result.datetime_utc      '2024-11-01 19:42:14' 
_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          8vmf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":504}' 
#
_entry.id    8VMF 
#
_exptl.entry_id    8VMF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          6 
_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            8VMF 
_cell.length_a            82.251 
_cell.length_b            82.251 
_cell.length_c            280.354 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8VMF 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    'P 61 2 (x,y,z+5/12)' 
_symmetry.space_group_name_H-M     'P 61 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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,M 
_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                      6 
_struct_asym.id                             G 
_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 161 A ASN 186 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? 
metalc ? metalc2 A OD2 ASP 175 A ASP 200 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.797 ? 
metalc ? metalc3 A OD1 ASP 175 A ASP 200 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.626 ? 
metalc ? metalc4 D MG MG . A MG 501 1_555 G O1B ADP . A ADP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? 
metalc ? metalc5 D MG MG . A MG 501 1_555 L O HOH . A HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.907 ? 
metalc ? metalc6 E MG MG . A MG 502 1_555 G O3B ADP . A ADP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? 
metalc ? metalc7 E MG MG . A MG 502 1_555 L O HOH . A HOH 647 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? 
#
_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                     8VMF 
_atom_sites.fract_transf_matrix[1][1]    0.012158 
_atom_sites.fract_transf_matrix[1][2]    0.007019 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014039 
_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]    0.003567 
_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
D 4 MG A 1 501 501 MG MG . 
E 4 MG A 1 502 502 MG MG . 
F 5 AF3 A 1 503 601 AF3 AF3 . 
G 6 ADP A 1 504 1 ADP ADP . 
H 7 GOL A 1 505 1 GOL GOL . 
I 7 GOL A 1 506 2 GOL GOL . 
J 7 GOL A 1 507 3 GOL GOL . 
K 8 CL A 1 508 1 CL CL . 
L 9 HOH A 1 601 120 HOH HOH . 
L 9 HOH A 2 602 119 HOH HOH . 
L 9 HOH A 3 603 38 HOH HOH . 
L 9 HOH A 4 604 165 HOH HOH . 
L 9 HOH A 5 605 123 HOH HOH . 
L 9 HOH A 6 606 144 HOH HOH . 
L 9 HOH A 7 607 162 HOH HOH . 
L 9 HOH A 8 608 167 HOH HOH . 
L 9 HOH A 9 609 160 HOH HOH . 
L 9 HOH A 10 610 82 HOH HOH . 
L 9 HOH A 11 611 153 HOH HOH . 
L 9 HOH A 12 612 86 HOH HOH . 
L 9 HOH A 13 613 37 HOH HOH . 
L 9 HOH A 14 614 58 HOH HOH . 
L 9 HOH A 15 615 35 HOH HOH . 
L 9 HOH A 16 616 81 HOH HOH . 
L 9 HOH A 17 617 135 HOH HOH . 
L 9 HOH A 18 618 142 HOH HOH . 
L 9 HOH A 19 619 158 HOH HOH . 
L 9 HOH A 20 620 21 HOH HOH . 
L 9 HOH A 21 621 51 HOH HOH . 
L 9 HOH A 22 622 161 HOH HOH . 
L 9 HOH A 23 623 19 HOH HOH . 
L 9 HOH A 24 624 166 HOH HOH . 
L 9 HOH A 25 625 107 HOH HOH . 
L 9 HOH A 26 626 77 HOH HOH . 
L 9 HOH A 27 627 133 HOH HOH . 
L 9 HOH A 28 628 25 HOH HOH . 
L 9 HOH A 29 629 3 HOH HOH . 
L 9 HOH A 30 630 96 HOH HOH . 
L 9 HOH A 31 631 117 HOH HOH . 
L 9 HOH A 32 632 61 HOH HOH . 
L 9 HOH A 33 633 66 HOH HOH . 
L 9 HOH A 34 634 18 HOH HOH . 
L 9 HOH A 35 635 164 HOH HOH . 
L 9 HOH A 36 636 70 HOH HOH . 
L 9 HOH A 37 637 15 HOH HOH . 
L 9 HOH A 38 638 68 HOH HOH . 
L 9 HOH A 39 639 141 HOH HOH . 
L 9 HOH A 40 640 126 HOH HOH . 
L 9 HOH A 41 641 44 HOH HOH . 
L 9 HOH A 42 642 22 HOH HOH . 
L 9 HOH A 43 643 69 HOH HOH . 
L 9 HOH A 44 644 159 HOH HOH . 
L 9 HOH A 45 645 131 HOH HOH . 
L 9 HOH A 46 646 163 HOH HOH . 
L 9 HOH A 47 647 129 HOH HOH . 
L 9 HOH A 48 648 5 HOH HOH . 
L 9 HOH A 49 649 14 HOH HOH . 
L 9 HOH A 50 650 102 HOH HOH . 
L 9 HOH A 51 651 17 HOH HOH . 
L 9 HOH A 52 652 168 HOH HOH . 
L 9 HOH A 53 653 13 HOH HOH . 
L 9 HOH A 54 654 97 HOH HOH . 
L 9 HOH A 55 655 46 HOH HOH . 
L 9 HOH A 56 656 26 HOH HOH . 
L 9 HOH A 57 657 31 HOH HOH . 
L 9 HOH A 58 658 95 HOH HOH . 
L 9 HOH A 59 659 62 HOH HOH . 
L 9 HOH A 60 660 152 HOH HOH . 
L 9 HOH A 61 661 4 HOH HOH . 
L 9 HOH A 62 662 10 HOH HOH . 
L 9 HOH A 63 663 73 HOH HOH . 
L 9 HOH A 64 664 57 HOH HOH . 
L 9 HOH A 65 665 88 HOH HOH . 
L 9 HOH A 66 666 169 HOH HOH . 
L 9 HOH A 67 667 8 HOH HOH . 
L 9 HOH A 68 668 23 HOH HOH . 
L 9 HOH A 69 669 56 HOH HOH . 
L 9 HOH A 70 670 6 HOH HOH . 
L 9 HOH A 71 671 9 HOH HOH . 
L 9 HOH A 72 672 138 HOH HOH . 
L 9 HOH A 73 673 49 HOH HOH . 
L 9 HOH A 74 674 34 HOH HOH . 
L 9 HOH A 75 675 12 HOH HOH . 
L 9 HOH A 76 676 24 HOH HOH . 
L 9 HOH A 77 677 2 HOH HOH . 
L 9 HOH A 78 678 125 HOH HOH . 
L 9 HOH A 79 679 92 HOH HOH . 
L 9 HOH A 80 680 16 HOH HOH . 
L 9 HOH A 81 681 83 HOH HOH . 
L 9 HOH A 82 682 1 HOH HOH . 
L 9 HOH A 83 683 122 HOH HOH . 
L 9 HOH A 84 684 63 HOH HOH . 
L 9 HOH A 85 685 124 HOH HOH . 
L 9 HOH A 86 686 7 HOH HOH . 
L 9 HOH A 87 687 40 HOH HOH . 
L 9 HOH A 88 688 106 HOH HOH . 
L 9 HOH A 89 689 150 HOH HOH . 
L 9 HOH A 90 690 116 HOH HOH . 
L 9 HOH A 91 691 84 HOH HOH . 
L 9 HOH A 92 692 76 HOH HOH . 
L 9 HOH A 93 693 59 HOH HOH . 
L 9 HOH A 94 694 121 HOH HOH . 
L 9 HOH A 95 695 157 HOH HOH . 
L 9 HOH A 96 696 101 HOH HOH . 
L 9 HOH A 97 697 50 HOH HOH . 
L 9 HOH A 98 698 65 HOH HOH . 
L 9 HOH A 99 699 33 HOH HOH . 
L 9 HOH A 100 700 105 HOH HOH . 
L 9 HOH A 101 701 154 HOH HOH . 
L 9 HOH A 102 702 74 HOH HOH . 
L 9 HOH A 103 703 149 HOH HOH . 
L 9 HOH A 104 704 115 HOH HOH . 
L 9 HOH A 105 705 155 HOH HOH . 
L 9 HOH A 106 706 98 HOH HOH . 
L 9 HOH A 107 707 127 HOH HOH . 
L 9 HOH A 108 708 45 HOH HOH . 
L 9 HOH A 109 709 118 HOH HOH . 
L 9 HOH A 110 710 139 HOH HOH . 
L 9 HOH A 111 711 113 HOH HOH . 
L 9 HOH A 112 712 85 HOH HOH . 
L 9 HOH A 113 713 104 HOH HOH . 
L 9 HOH A 114 714 93 HOH HOH . 
L 9 HOH A 115 715 103 HOH HOH . 
L 9 HOH A 116 716 134 HOH HOH . 
L 9 HOH A 117 717 11 HOH HOH . 
L 9 HOH A 118 718 55 HOH HOH . 
L 9 HOH A 119 719 136 HOH HOH . 
L 9 HOH A 120 720 112 HOH HOH . 
L 9 HOH A 121 721 109 HOH HOH . 
L 9 HOH A 122 722 137 HOH HOH . 
M 9 HOH B 1 501 27 HOH HOH . 
M 9 HOH B 2 502 78 HOH HOH . 
M 9 HOH B 3 503 128 HOH HOH . 
M 9 HOH B 4 504 29 HOH HOH . 
M 9 HOH B 5 505 47 HOH HOH . 
M 9 HOH B 6 506 20 HOH HOH . 
M 9 HOH B 7 507 91 HOH HOH . 
M 9 HOH B 8 508 156 HOH HOH . 
M 9 HOH B 9 509 48 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 . . . G 6 10.966 -45.427 -12.243 0.82 100.19 ? PB ADP 504 A 1 
HETATM 2 O O1B ADP . . . G 6 9.577 -45.411 -12.84 0.82 100.53 ? O1B ADP 504 A 1 
HETATM 3 O O2B ADP . . . G 6 11.184 -46.48 -11.182 0.82 100.18 ? O2B ADP 504 A 1 
HETATM 4 O O3B ADP . . . G 6 12.077 -45.35 -13.264 0.82 102.33 ? O3B ADP 504 A 1 
HETATM 5 P PA ADP . . . G 6 10.407 -43.728 -10.02 0.82 94.92 ? PA ADP 504 A 1 
HETATM 6 O O1A ADP . . . G 6 10.758 -42.308 -9.648 0.82 93.33 ? O1A ADP 504 A 1 
HETATM 7 O O2A ADP . . . G 6 10.763 -44.838 -9.062 0.82 95.23 ? O2A ADP 504 A 1 
HETATM 8 O O3A ADP . . . G 6 11.079 -44.024 -11.455 0.82 97.46 ? O3A ADP 504 A 1 
HETATM 9 O O5' ADP . . . G 6 8.817 -43.777 -10.261 0.82 94.66 ? O5' ADP 504 A 1 
HETATM 10 C C5' ADP . . . G 6 8.116 -45.019 -10.284 0.82 95.89 ? C5' ADP 504 A 1 
HETATM 11 C C4' ADP . . . G 6 6.872 -44.899 -9.412 0.82 94.45 ? C4' ADP 504 A 1 
HETATM 12 O O4' ADP . . . G 6 7.258 -44.888 -8.035 0.82 92.97 ? O4' ADP 504 A 1 
HETATM 13 C C3' ADP . . . G 6 6.104 -43.614 -9.682 0.82 93.35 ? C3' ADP 504 A 1 
HETATM 14 O O3' ADP . . . G 6 4.915 -43.875 -10.436 0.82 94.71 ? O3' ADP 504 A 1 
HETATM 15 C C2' ADP . . . G 6 5.751 -43.065 -8.315 0.82 91.21 ? C2' ADP 504 A 1 
HETATM 16 O O2' ADP . . . G 6 4.342 -43.186 -8.102 0.82 91.22 ? O2' ADP 504 A 1 
HETATM 17 C C1' ADP . . . G 6 6.515 -43.911 -7.303 0.82 91.07 ? C1' ADP 504 A 1 
HETATM 18 N N9 ADP . . . G 6 7.448 -43.025 -6.561 0.82 89.69 ? N9 ADP 504 A 1 
HETATM 19 C C8 ADP . . . G 6 8.678 -42.661 -6.976 0.82 90.04 ? C8 ADP 504 A 1 
HETATM 20 N N7 ADP . . . G 6 9.28 -41.837 -6.082 0.82 88.89 ? N7 ADP 504 A 1 
HETATM 21 C C5 ADP . . . G 6 8.42 -41.659 -5.064 0.82 87.76 ? C5 ADP 504 A 1 
HETATM 22 C C6 ADP . . . G 6 8.419 -40.902 -3.792 0.82 86.6 ? C6 ADP 504 A 1 
HETATM 23 N N6 ADP . . . G 6 9.485 -40.156 -3.419 0.82 86.46 ? N6 ADP 504 A 1 
HETATM 24 N N1 ADP . . . G 6 7.318 -40.985 -3.018 0.82 86.02 ? N1 ADP 504 A 1 
HETATM 25 C C2 ADP . . . G 6 6.255 -41.726 -3.371 0.82 86.47 ? C2 ADP 504 A 1 
HETATM 26 N N3 ADP . . . G 6 6.183 -42.437 -4.506 0.82 87.57 ? N3 ADP 504 A 1 
HETATM 27 C C4 ADP . . . G 6 7.215 -42.442 -5.382 0.82 88.26 ? C4 ADP 504 A 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           299 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           27 
#