data_4WTD
#
_model_server_result.job_id            8rR4AitLW5ruNIjwjr7wcw 
_model_server_result.datetime_utc      '2024-11-09 02:16:19' 
_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          4wtd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":602}' 
#
_entry.id    4WTD 
#
_exptl.entry_id    4WTD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          4 
_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            4WTD 
_cell.length_a            141.25 
_cell.length_b            141.25 
_cell.length_c            91.19 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4WTD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        170 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_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 
_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                      4 
_struct_asym.id                             E 
_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 B O3' U 8 P U 8 1_555 D MN MN . P MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? 
metalc ? metalc2 D MN MN . P MN 601 1_555 E O1A ADP . P ADP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? 
metalc ? metalc3 D MN MN . P MN 601 1_555 J O HOH . P HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? 
metalc ? metalc4 D MN MN . P MN 601 1_555 C OD1 ASP 222 A ASP 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? 
metalc ? metalc5 D MN MN . P MN 601 1_555 C OD1 ASP 320 A ASP 318 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? 
metalc ? metalc6 D MN MN . P MN 601 1_555 C OD1 ASP 321 A ASP 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? 
metalc ? metalc7 E O1B ADP . P ADP 602 1_555 F MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
metalc ? metalc8 E O1A ADP . P ADP 602 1_555 F MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? 
metalc ? metalc9 J O HOH . P HOH 705 1_555 F MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? 
metalc ? metalc10 C OD2 ASP 222 A ASP 220 1_555 F MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? 
metalc ? metalc11 C O THR 223 A THR 221 1_555 F MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? 
metalc ? metalc12 C OE2 GLU 239 A GLU 237 1_555 G MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.894 ? 
metalc ? metalc13 C ND1 HIS 256 A HIS 254 1_555 G MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
metalc ? metalc14 C OD2 ASP 320 A ASP 318 1_555 F MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? 
hydrog WATSON-CRICK hydrog1 A N1 A 3 T A 3 1_555 B N3 U 8 P U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A N6 A 3 T A 3 1_555 B O4 U 8 P U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A N1 A 4 T A 4 1_555 B N3 U 7 P U 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 A N6 A 4 T A 4 1_555 B O4 U 7 P U 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 A N1 A 5 T A 5 1_555 B N3 U 6 P U 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 A N6 A 5 T A 5 1_555 B O4 U 6 P U 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 A N3 U 6 T U 6 1_555 B N1 A 5 P A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 A O4 U 6 T U 6 1_555 B N6 A 5 P A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 A N3 U 7 T U 7 1_555 B N1 A 4 P A 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 A O4 U 7 T U 7 1_555 B N6 A 4 P A 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_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 40 n n 
PB O2B ADP sing 41 n n 
PB O3B ADP sing 42 n n 
PB O3A ADP sing 43 n n 
O2B HOB2 ADP sing 44 n n 
O3B HOB3 ADP sing 45 n n 
PA O1A ADP doub 46 n n 
PA O2A ADP sing 47 n n 
PA O3A ADP sing 48 n n 
PA O5' ADP sing 49 n n 
O2A HOA2 ADP sing 50 n n 
O5' C5' ADP sing 51 n n 
C5' C4' ADP sing 52 n n 
C5' "H5'1" ADP sing 53 n n 
C5' "H5'2" ADP sing 54 n n 
C4' O4' ADP sing 55 n n 
C4' C3' ADP sing 56 n n 
C4' H4' ADP sing 57 n n 
O4' C1' ADP sing 58 n n 
C3' O3' ADP sing 59 n n 
C3' C2' ADP sing 60 n n 
C3' H3' ADP sing 61 n n 
O3' HO3' ADP sing 62 n n 
C2' O2' ADP sing 63 n n 
C2' C1' ADP sing 64 n n 
C2' H2' ADP sing 65 n n 
O2' HO2' ADP sing 66 n n 
C1' N9 ADP sing 67 n n 
C1' H1' ADP sing 68 n n 
N9 C8 ADP sing 69 n y 
N9 C4 ADP sing 70 n y 
C8 N7 ADP doub 71 n y 
C8 H8 ADP sing 72 n n 
N7 C5 ADP sing 73 n y 
C5 C6 ADP sing 74 n y 
C5 C4 ADP doub 75 n y 
C6 N6 ADP sing 76 n n 
C6 N1 ADP doub 77 n y 
N6 HN61 ADP sing 78 n n 
N6 HN62 ADP sing 79 n n 
N1 C2 ADP sing 80 n y 
C2 N3 ADP doub 81 n y 
C2 H2 ADP sing 82 n n 
N3 C4 ADP sing 83 n y 
#
_atom_sites.entry_id                     4WTD 
_atom_sites.fract_transf_matrix[1][1]    0.00708 
_atom_sites.fract_transf_matrix[1][2]    0.004087 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008175 
_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]    0.010966 
_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 3 MN P 1 601 1 MN MN . 
E 4 ADP P 1 602 1 ADP ADP . 
F 3 MN A 1 601 2 MN MN . 
G 3 MN A 1 602 3 MN MN . 
H 5 CL A 1 603 1 CL CL . 
I 6 HOH T 1 101 51 HOH HOH . 
J 6 HOH P 1 701 45 HOH HOH . 
J 6 HOH P 2 702 46 HOH HOH . 
J 6 HOH P 3 703 47 HOH HOH . 
J 6 HOH P 4 704 1 HOH HOH . 
J 6 HOH P 5 705 2 HOH HOH . 
K 6 HOH A 1 701 48 HOH HOH . 
K 6 HOH A 2 702 40 HOH HOH . 
K 6 HOH A 3 703 49 HOH HOH . 
K 6 HOH A 4 704 5 HOH HOH . 
K 6 HOH A 5 705 24 HOH HOH . 
K 6 HOH A 6 706 28 HOH HOH . 
K 6 HOH A 7 707 8 HOH HOH . 
K 6 HOH A 8 708 22 HOH HOH . 
K 6 HOH A 9 709 3 HOH HOH . 
K 6 HOH A 10 710 4 HOH HOH . 
K 6 HOH A 11 711 6 HOH HOH . 
K 6 HOH A 12 712 7 HOH HOH . 
K 6 HOH A 13 713 9 HOH HOH . 
K 6 HOH A 14 714 10 HOH HOH . 
K 6 HOH A 15 715 11 HOH HOH . 
K 6 HOH A 16 716 12 HOH HOH . 
K 6 HOH A 17 717 13 HOH HOH . 
K 6 HOH A 18 718 14 HOH HOH . 
K 6 HOH A 19 719 15 HOH HOH . 
K 6 HOH A 20 720 16 HOH HOH . 
K 6 HOH A 21 721 17 HOH HOH . 
K 6 HOH A 22 722 18 HOH HOH . 
K 6 HOH A 23 723 19 HOH HOH . 
K 6 HOH A 24 724 20 HOH HOH . 
K 6 HOH A 25 725 21 HOH HOH . 
K 6 HOH A 26 726 23 HOH HOH . 
K 6 HOH A 27 727 25 HOH HOH . 
K 6 HOH A 28 728 26 HOH HOH . 
K 6 HOH A 29 729 27 HOH HOH . 
K 6 HOH A 30 730 29 HOH HOH . 
K 6 HOH A 31 731 30 HOH HOH . 
K 6 HOH A 32 732 31 HOH HOH . 
K 6 HOH A 33 733 32 HOH HOH . 
K 6 HOH A 34 734 33 HOH HOH . 
K 6 HOH A 35 735 34 HOH HOH . 
K 6 HOH A 36 736 35 HOH HOH . 
K 6 HOH A 37 737 36 HOH HOH . 
K 6 HOH A 38 738 37 HOH HOH . 
K 6 HOH A 39 739 38 HOH HOH . 
K 6 HOH A 40 740 39 HOH HOH . 
K 6 HOH A 41 741 41 HOH HOH . 
K 6 HOH A 42 742 42 HOH HOH . 
K 6 HOH A 43 743 43 HOH HOH . 
K 6 HOH A 44 744 44 HOH HOH . 
K 6 HOH A 45 745 50 HOH HOH . 
K 6 HOH A 46 746 52 HOH HOH . 
K 6 HOH A 47 747 53 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 . . . E 4 42.627 -43.081 2.518 1 43.37 ? PB ADP 602 P 1 
HETATM 2 O O1B ADP . . . E 4 42.735 -44.071 1.366 1 32.73 ? O1B ADP 602 P 1 
HETATM 3 O O2B ADP . . . E 4 43.201 -41.687 2.353 1 43.45 ? O2B ADP 602 P 1 
HETATM 4 O O3B ADP . . . E 4 41.214 -42.861 3.031 1 44.51 ? O3B ADP 602 P 1 
HETATM 5 P PA ADP . . . E 4 44.194 -45.132 3.836 1 42.74 ? PA ADP 602 P 1 
HETATM 6 O O1A ADP . . . E 4 44.704 -45.564 2.485 1 45.41 ? O1A ADP 602 P 1 
HETATM 7 O O2A ADP . . . E 4 45.08 -45.299 5.008 1 45.8 ? O2A ADP 602 P 1 
HETATM 8 O O3A ADP . . . E 4 43.538 -43.664 3.738 1 41.52 ? O3A ADP 602 P 1 
HETATM 9 O O5' ADP . . . E 4 42.886 -45.924 4.317 1 49.34 ? O5' ADP 602 P 1 
HETATM 10 C C5' ADP . . . E 4 41.973 -46.551 3.405 1 47.18 ? C5' ADP 602 P 1 
HETATM 11 C C4' ADP . . . E 4 40.552 -46.618 3.984 1 45.37 ? C4' ADP 602 P 1 
HETATM 12 O O4' ADP . . . E 4 40.49 -47.466 5.148 1 45.53 ? O4' ADP 602 P 1 
HETATM 13 C C3' ADP . . . E 4 39.944 -45.295 4.427 1 45.72 ? C3' ADP 602 P 1 
HETATM 14 O O3' ADP . . . E 4 39.363 -44.537 3.36 1 43.21 ? O3' ADP 602 P 1 
HETATM 15 C C2' ADP . . . E 4 38.909 -45.762 5.436 1 46.68 ? C2' ADP 602 P 1 
HETATM 16 O O2' ADP . . . E 4 37.696 -46.194 4.789 1 50.93 ? O2' ADP 602 P 1 
HETATM 17 C C1' ADP . . . E 4 39.596 -46.943 6.116 1 45.15 ? C1' ADP 602 P 1 
HETATM 18 N N9 ADP . . . E 4 40.254 -46.361 7.306 1 46.36 ? N9 ADP 602 P 1 
HETATM 19 C C8 ADP . . . E 4 41.503 -45.861 7.477 1 45.82 ? C8 ADP 602 P 1 
HETATM 20 N N7 ADP . . . E 4 41.663 -45.373 8.745 1 44.93 ? N7 ADP 602 P 1 
HETATM 21 C C5 ADP . . . E 4 40.486 -45.565 9.391 1 46.09 ? C5 ADP 602 P 1 
HETATM 22 C C6 ADP . . . E 4 39.893 -45.317 10.733 1 45.52 ? C6 ADP 602 P 1 
HETATM 23 N N6 ADP . . . E 4 40.584 -44.728 11.735 1 43.31 ? N6 ADP 602 P 1 
HETATM 24 N N1 ADP . . . E 4 38.617 -45.707 10.96 1 46.07 ? N1 ADP 602 P 1 
HETATM 25 C C2 ADP . . . E 4 37.877 -46.284 10.013 1 46.04 ? C2 ADP 602 P 1 
HETATM 26 N N3 ADP . . . E 4 38.331 -46.53 8.785 1 44.07 ? N3 ADP 602 P 1 
HETATM 27 C C4 ADP . . . E 4 39.582 -46.206 8.428 1 46.88 ? C4 ADP 602 P 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           297 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#