data_5LXM
#
_model_server_result.job_id            Qd5aWqpwbykbsSc7Dq3zVQ 
_model_server_result.datetime_utc      '2024-11-25 08:33:36' 
_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          5lxm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":501}' 
#
_entry.id    5LXM 
#
_exptl.entry_id    5LXM 
_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         120 
_cell.entry_id            5LXM 
_cell.length_a            79.78 
_cell.length_b            79.78 
_cell.length_c            140.26 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5LXM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31 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,G,H,I,J,K,L,M,N 
_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                             C 
_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 167 A THR 287 1_555 A N TPO 168 A TPO 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale2 A C TPO 168 A TPO 288 1_555 A N LEU 169 A LEU 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale3 B C GLU 31 D GLU 36 1_555 B N MK8 32 D MK8 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
covale ? covale4 B C MK8 32 D MK8 37 1_555 B N LYS 33 D LYS 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale5 B CE MK8 32 D MK8 37 1_555 B CE MK8 36 D MK8 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale6 B C ASN 35 D ASN 40 1_555 B N MK8 36 D MK8 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
covale ? covale7 B C MK8 36 D MK8 41 1_555 B N GLU 37 D GLU 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale8 B C ASN 38 D ASN 43 1_555 B N NH2 39 D NH2 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
metalc ? metalc1 A OD1 ASN 141 A ASN 261 1_555 K MG MG . A MG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.67 ? 
metalc ? metalc2 A OD2 ASP 154 A ASP 274 1_555 K MG MG . A MG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? 
metalc ? metalc3 A OD1 ASP 154 A ASP 274 1_555 L MG MG . A MG 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? 
metalc ? metalc4 C O3B ADP . A ADP 501 1_555 K MG MG . A MG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? 
metalc ? metalc5 C O2A ADP . A ADP 501 1_555 K MG MG . A MG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? 
metalc ? metalc6 C O1B ADP . A ADP 501 1_555 L MG MG . A MG 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? 
metalc ? metalc7 G O4 PEG . A PEG 505 1_555 L MG MG . A MG 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.939 ? 
metalc ? metalc8 K MG MG . A MG 509 1_555 M O HOH . A HOH 651 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
metalc ? metalc9 K MG MG . A MG 509 1_555 M O HOH . A HOH 654 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? 
metalc ? metalc10 L MG MG . A MG 510 1_555 M O HOH . A HOH 631 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? 
#
_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                     5LXM 
_atom_sites.fract_transf_matrix[1][1]    0.012534 
_atom_sites.fract_transf_matrix[1][2]    0.007237 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014474 
_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]    0.00713 
_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 3 ADP A 1 501 1 ADP ADP . 
D 4 PG4 A 1 502 1 PG4 P6G . 
E 5 SO4 A 1 503 1 SO4 SO4 . 
F 6 PEG A 1 504 1 PEG PEG . 
G 6 PEG A 1 505 2 PEG PEG . 
H 7 MES A 1 506 1 MES MES . 
I 8 P4G A 1 507 1 P4G P4G . 
J 9 CL A 1 508 1 CL CL . 
K 10 MG A 1 509 3 MG MG . 
L 10 MG A 1 510 4 MG MG . 
M 11 HOH A 1 601 33 HOH HOH . 
M 11 HOH A 2 602 35 HOH HOH . 
M 11 HOH A 3 603 108 HOH HOH . 
M 11 HOH A 4 604 37 HOH HOH . 
M 11 HOH A 5 605 23 HOH HOH . 
M 11 HOH A 6 606 6 HOH HOH . 
M 11 HOH A 7 607 115 HOH HOH . 
M 11 HOH A 8 608 49 HOH HOH . 
M 11 HOH A 9 609 14 HOH HOH . 
M 11 HOH A 10 610 189 HOH HOH . 
M 11 HOH A 11 611 128 HOH HOH . 
M 11 HOH A 12 612 172 HOH HOH . 
M 11 HOH A 13 613 105 HOH HOH . 
M 11 HOH A 14 614 11 HOH HOH . 
M 11 HOH A 15 615 113 HOH HOH . 
M 11 HOH A 16 616 114 HOH HOH . 
M 11 HOH A 17 617 18 HOH HOH . 
M 11 HOH A 18 618 153 HOH HOH . 
M 11 HOH A 19 619 3 HOH HOH . 
M 11 HOH A 20 620 17 HOH HOH . 
M 11 HOH A 21 621 147 HOH HOH . 
M 11 HOH A 22 622 24 HOH HOH . 
M 11 HOH A 23 623 4 HOH HOH . 
M 11 HOH A 24 624 203 HOH HOH . 
M 11 HOH A 25 625 39 HOH HOH . 
M 11 HOH A 26 626 188 HOH HOH . 
M 11 HOH A 27 627 127 HOH HOH . 
M 11 HOH A 28 628 22 HOH HOH . 
M 11 HOH A 29 629 111 HOH HOH . 
M 11 HOH A 30 630 34 HOH HOH . 
M 11 HOH A 31 631 205 HOH HOH . 
M 11 HOH A 32 632 80 HOH HOH . 
M 11 HOH A 33 633 16 HOH HOH . 
M 11 HOH A 34 634 15 HOH HOH . 
M 11 HOH A 35 635 7 HOH HOH . 
M 11 HOH A 36 636 50 HOH HOH . 
M 11 HOH A 37 637 10 HOH HOH . 
M 11 HOH A 38 638 13 HOH HOH . 
M 11 HOH A 39 639 136 HOH HOH . 
M 11 HOH A 40 640 110 HOH HOH . 
M 11 HOH A 41 641 19 HOH HOH . 
M 11 HOH A 42 642 32 HOH HOH . 
M 11 HOH A 43 643 200 HOH HOH . 
M 11 HOH A 44 644 20 HOH HOH . 
M 11 HOH A 45 645 5 HOH HOH . 
M 11 HOH A 46 646 204 HOH HOH . 
M 11 HOH A 47 647 36 HOH HOH . 
M 11 HOH A 48 648 132 HOH HOH . 
M 11 HOH A 49 649 143 HOH HOH . 
M 11 HOH A 50 650 25 HOH HOH . 
M 11 HOH A 51 651 202 HOH HOH . 
M 11 HOH A 52 652 116 HOH HOH . 
M 11 HOH A 53 653 38 HOH HOH . 
M 11 HOH A 54 654 201 HOH HOH . 
M 11 HOH A 55 655 8 HOH HOH . 
M 11 HOH A 56 656 74 HOH HOH . 
M 11 HOH A 57 657 45 HOH HOH . 
M 11 HOH A 58 658 101 HOH HOH . 
M 11 HOH A 59 659 126 HOH HOH . 
M 11 HOH A 60 660 181 HOH HOH . 
M 11 HOH A 61 661 117 HOH HOH . 
M 11 HOH A 62 662 99 HOH HOH . 
M 11 HOH A 63 663 184 HOH HOH . 
M 11 HOH A 64 664 106 HOH HOH . 
M 11 HOH A 65 665 121 HOH HOH . 
M 11 HOH A 66 666 86 HOH HOH . 
M 11 HOH A 67 667 66 HOH HOH . 
M 11 HOH A 68 668 195 HOH HOH . 
M 11 HOH A 69 669 76 HOH HOH . 
M 11 HOH A 70 670 100 HOH HOH . 
N 11 HOH D 1 201 196 HOH HOH . 
N 11 HOH D 2 202 62 HOH HOH . 
N 11 HOH D 3 203 61 HOH HOH . 
N 11 HOH D 4 204 144 HOH HOH . 
N 11 HOH D 5 205 63 HOH HOH . 
N 11 HOH D 6 206 134 HOH HOH . 
N 11 HOH D 7 207 197 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 . . . C 3 52.911 -10.013 11.891 1 163.92 ? PB ADP 501 A 1 
HETATM 2 O O1B ADP . . . C 3 52.391 -10.824 10.73 1 169.8 ? O1B ADP 501 A 1 
HETATM 3 O O2B ADP . . . C 3 53.85 -8.904 11.481 1 165.38 ? O2B ADP 501 A 1 
HETATM 4 O O3B ADP . . . C 3 53.369 -10.828 13.077 1 156.95 ? O3B ADP 501 A 1 
HETATM 5 P PA ADP . . . C 3 50.257 -9.985 12.875 1 78.32 ? PA ADP 501 A 1 
HETATM 6 O O1A ADP . . . C 3 49.181 -9.73 11.846 1 74.18 ? O1A ADP 501 A 1 
HETATM 7 O O2A ADP . . . C 3 50.54 -11.394 13.333 1 84.03 ? O2A ADP 501 A 1 
HETATM 8 O O3A ADP . . . C 3 51.619 -9.234 12.451 1 62.39 ? O3A ADP 501 A 1 
HETATM 9 O O5' ADP . . . C 3 49.91 -9.149 14.201 1 93.8 ? O5' ADP 501 A 1 
HETATM 10 C C5' ADP . . . C 3 48.979 -8.082 14.137 1 85.32 ? C5' ADP 501 A 1 
HETATM 11 C C4' ADP . . . C 3 48.337 -7.881 15.495 1 80.05 ? C4' ADP 501 A 1 
HETATM 12 O O4' ADP . . . C 3 47.182 -7.066 15.294 1 73.59 ? O4' ADP 501 A 1 
HETATM 13 C C3' ADP . . . C 3 47.862 -9.199 16.084 1 83.67 ? C3' ADP 501 A 1 
HETATM 14 O O3' ADP . . . C 3 48.724 -9.645 17.136 1 88.88 ? O3' ADP 501 A 1 
HETATM 15 C C2' ADP . . . C 3 46.475 -8.895 16.604 1 84.18 ? C2' ADP 501 A 1 
HETATM 16 O O2' ADP . . . C 3 46.568 -8.501 17.975 1 81.25 ? O2' ADP 501 A 1 
HETATM 17 C C1' ADP . . . C 3 46.006 -7.703 15.793 1 77.25 ? C1' ADP 501 A 1 
HETATM 18 N N9 ADP . . . C 3 45.203 -8.177 14.636 1 68.46 ? N9 ADP 501 A 1 
HETATM 19 C C8 ADP . . . C 3 45.706 -8.681 13.49 1 70.38 ? C8 ADP 501 A 1 
HETATM 20 N N7 ADP . . . C 3 44.724 -9.027 12.622 1 66.74 ? N7 ADP 501 A 1 
HETATM 21 C C5 ADP . . . C 3 43.552 -8.74 13.214 1 65.12 ? C5 ADP 501 A 1 
HETATM 22 C C6 ADP . . . C 3 42.124 -8.86 12.844 1 66.97 ? C6 ADP 501 A 1 
HETATM 23 N N6 ADP . . . C 3 41.758 -9.366 11.64 1 63.84 ? N6 ADP 501 A 1 
HETATM 24 N N1 ADP . . . C 3 41.204 -8.449 13.745 1 57.19 ? N1 ADP 501 A 1 
HETATM 25 C C2 ADP . . . C 3 41.568 -7.946 14.94 1 62.2 ? C2 ADP 501 A 1 
HETATM 26 N N3 ADP . . . C 3 42.846 -7.81 15.34 1 50.79 ? N3 ADP 501 A 1 
HETATM 27 C C4 ADP . . . C 3 43.87 -8.183 14.539 1 64.89 ? C4 ADP 501 A 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           323 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           27 
#