data_4NM7
#
_model_server_result.job_id            -EzqgDZXYmQ_dA2jt9062w 
_model_server_result.datetime_utc      '2024-11-27 03:20:38' 
_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          4nm7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":401}' 
#
_entry.id    4NM7 
#
_exptl.entry_id    4NM7 
_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            4NM7 
_cell.length_a            82.002 
_cell.length_b            82.002 
_cell.length_c            280.345 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4NM7 
_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    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,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                      4 
_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
covale ? covale1 C C PRO 5 C PRO 1606 1_555 C N SEP 6 C SEP 1607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale2 C C SEP 6 C SEP 1607 1_555 C N PRO 7 C PRO 1608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? 
metalc ? metalc1 A OD1 ASN 174 A ASN 186 1_555 I MG MG . A MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? 
metalc ? metalc2 A OD1 ASP 188 A ASP 200 1_555 H MG MG . A MG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? 
metalc ? metalc3 A OD2 ASP 188 A ASP 200 1_555 I MG MG . A MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? 
metalc ? metalc4 D O2B ADP . A ADP 401 1_555 H MG MG . A MG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? 
metalc ? metalc5 D O1A ADP . A ADP 401 1_555 I MG MG . A MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? 
metalc ? metalc6 D O1B ADP . A ADP 401 1_555 I MG MG . A MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? 
metalc ? metalc7 H MG MG . A MG 405 1_555 L O HOH . A HOH 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.918 ? 
metalc ? metalc8 H MG MG . A MG 405 1_555 L O HOH . A HOH 539 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.558 ? 
metalc ? metalc9 I MG MG . A MG 406 1_555 L O HOH . A HOH 571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? 
metalc ? metalc10 I MG MG . A MG 406 1_555 L O HOH . A HOH 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? 
#
_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                     4NM7 
_atom_sites.fract_transf_matrix[1][1]    0.012195 
_atom_sites.fract_transf_matrix[1][2]    0.007041 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014081 
_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 ADP A 1 401 1 ADP ADP . 
E 5 GOL A 1 402 1 GOL GOL . 
F 5 GOL A 1 403 2 GOL GOL . 
G 5 GOL A 1 404 4 GOL GOL . 
H 6 MG A 1 405 1 MG MG . 
I 6 MG A 1 406 2 MG MG . 
J 7 CL A 1 407 1 CL CL . 
K 8 DTT A 1 408 1 DTT DTT . 
L 9 HOH A 1 501 1 HOH HOH . 
L 9 HOH A 2 502 2 HOH HOH . 
L 9 HOH A 3 503 3 HOH HOH . 
L 9 HOH A 4 504 4 HOH HOH . 
L 9 HOH A 5 505 5 HOH HOH . 
L 9 HOH A 6 506 6 HOH HOH . 
L 9 HOH A 7 507 7 HOH HOH . 
L 9 HOH A 8 508 8 HOH HOH . 
L 9 HOH A 9 509 9 HOH HOH . 
L 9 HOH A 10 510 10 HOH HOH . 
L 9 HOH A 11 511 11 HOH HOH . 
L 9 HOH A 12 512 12 HOH HOH . 
L 9 HOH A 13 513 13 HOH HOH . 
L 9 HOH A 14 514 14 HOH HOH . 
L 9 HOH A 15 515 15 HOH HOH . 
L 9 HOH A 16 516 16 HOH HOH . 
L 9 HOH A 17 517 17 HOH HOH . 
L 9 HOH A 18 518 18 HOH HOH . 
L 9 HOH A 19 519 19 HOH HOH . 
L 9 HOH A 20 520 20 HOH HOH . 
L 9 HOH A 21 521 21 HOH HOH . 
L 9 HOH A 22 522 22 HOH HOH . 
L 9 HOH A 23 523 23 HOH HOH . 
L 9 HOH A 24 524 25 HOH HOH . 
L 9 HOH A 25 525 26 HOH HOH . 
L 9 HOH A 26 526 27 HOH HOH . 
L 9 HOH A 27 527 28 HOH HOH . 
L 9 HOH A 28 528 29 HOH HOH . 
L 9 HOH A 29 529 30 HOH HOH . 
L 9 HOH A 30 530 31 HOH HOH . 
L 9 HOH A 31 531 32 HOH HOH . 
L 9 HOH A 32 532 33 HOH HOH . 
L 9 HOH A 33 533 34 HOH HOH . 
L 9 HOH A 34 534 35 HOH HOH . 
L 9 HOH A 35 535 36 HOH HOH . 
L 9 HOH A 36 536 37 HOH HOH . 
L 9 HOH A 37 537 38 HOH HOH . 
L 9 HOH A 38 538 39 HOH HOH . 
L 9 HOH A 39 539 40 HOH HOH . 
L 9 HOH A 40 540 41 HOH HOH . 
L 9 HOH A 41 541 42 HOH HOH . 
L 9 HOH A 42 542 44 HOH HOH . 
L 9 HOH A 43 543 45 HOH HOH . 
L 9 HOH A 44 544 46 HOH HOH . 
L 9 HOH A 45 545 47 HOH HOH . 
L 9 HOH A 46 546 48 HOH HOH . 
L 9 HOH A 47 547 49 HOH HOH . 
L 9 HOH A 48 548 50 HOH HOH . 
L 9 HOH A 49 549 52 HOH HOH . 
L 9 HOH A 50 550 54 HOH HOH . 
L 9 HOH A 51 551 55 HOH HOH . 
L 9 HOH A 52 552 56 HOH HOH . 
L 9 HOH A 53 553 60 HOH HOH . 
L 9 HOH A 54 554 61 HOH HOH . 
L 9 HOH A 55 555 62 HOH HOH . 
L 9 HOH A 56 556 63 HOH HOH . 
L 9 HOH A 57 557 64 HOH HOH . 
L 9 HOH A 58 558 65 HOH HOH . 
L 9 HOH A 59 559 67 HOH HOH . 
L 9 HOH A 60 560 69 HOH HOH . 
L 9 HOH A 61 561 70 HOH HOH . 
L 9 HOH A 62 562 71 HOH HOH . 
L 9 HOH A 63 563 72 HOH HOH . 
L 9 HOH A 64 564 73 HOH HOH . 
L 9 HOH A 65 565 74 HOH HOH . 
L 9 HOH A 66 566 75 HOH HOH . 
L 9 HOH A 67 567 76 HOH HOH . 
L 9 HOH A 68 568 77 HOH HOH . 
L 9 HOH A 69 569 79 HOH HOH . 
L 9 HOH A 70 570 81 HOH HOH . 
L 9 HOH A 71 571 82 HOH HOH . 
L 9 HOH A 72 572 83 HOH HOH . 
L 9 HOH A 73 573 84 HOH HOH . 
L 9 HOH A 74 574 85 HOH HOH . 
L 9 HOH A 75 575 86 HOH HOH . 
L 9 HOH A 76 576 87 HOH HOH . 
L 9 HOH A 77 577 88 HOH HOH . 
L 9 HOH A 78 578 89 HOH HOH . 
L 9 HOH A 79 579 91 HOH HOH . 
L 9 HOH A 80 580 92 HOH HOH . 
L 9 HOH A 81 581 93 HOH HOH . 
L 9 HOH A 82 582 94 HOH HOH . 
L 9 HOH A 83 583 95 HOH HOH . 
L 9 HOH A 84 584 96 HOH HOH . 
L 9 HOH A 85 585 97 HOH HOH . 
L 9 HOH A 86 586 98 HOH HOH . 
L 9 HOH A 87 587 99 HOH HOH . 
L 9 HOH A 88 588 100 HOH HOH . 
L 9 HOH A 89 589 101 HOH HOH . 
L 9 HOH A 90 590 102 HOH HOH . 
L 9 HOH A 91 591 103 HOH HOH . 
L 9 HOH A 92 592 104 HOH HOH . 
L 9 HOH A 93 593 105 HOH HOH . 
L 9 HOH A 94 594 106 HOH HOH . 
L 9 HOH A 95 595 107 HOH HOH . 
M 9 HOH B 1 501 24 HOH HOH . 
M 9 HOH B 2 502 43 HOH HOH . 
M 9 HOH B 3 503 51 HOH HOH . 
M 9 HOH B 4 504 53 HOH HOH . 
M 9 HOH B 5 505 57 HOH HOH . 
M 9 HOH B 6 506 58 HOH HOH . 
M 9 HOH B 7 507 59 HOH HOH . 
M 9 HOH B 8 508 66 HOH HOH . 
M 9 HOH B 9 509 78 HOH HOH . 
M 9 HOH B 10 510 80 HOH HOH . 
N 9 HOH C 1 1701 68 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 4 -10.628 45.077 -12.374 0.72 58.2 ? PB ADP 401 A 1 
HETATM 2 O O1B ADP . . . D 4 -9.447 44.735 -13.253 0.72 57.15 ? O1B ADP 401 A 1 
HETATM 3 O O2B ADP . . . D 4 -11.862 44.373 -12.881 0.72 58 ? O2B ADP 401 A 1 
HETATM 4 O O3B ADP . . . D 4 -10.87 46.566 -12.415 0.72 57.72 ? O3B ADP 401 A 1 
HETATM 5 P PA ADP . . . D 4 -9.736 43.282 -10.392 0.72 54.16 ? PA ADP 401 A 1 
HETATM 6 O O1A ADP . . . D 4 -9.021 42.588 -11.526 0.72 58.28 ? O1A ADP 401 A 1 
HETATM 7 O O2A ADP . . . D 4 -10.807 42.371 -9.84 0.72 43.45 ? O2A ADP 401 A 1 
HETATM 8 O O3A ADP . . . D 4 -10.337 44.663 -10.879 0.72 100.9 ? O3A ADP 401 A 1 
HETATM 9 O O5' ADP . . . D 4 -8.672 43.629 -9.283 0.72 57.72 ? O5' ADP 401 A 1 
HETATM 10 C C5' ADP . . . D 4 -7.792 44.686 -9.585 0.72 54.49 ? C5' ADP 401 A 1 
HETATM 11 C C4' ADP . . . D 4 -6.489 44.44 -8.952 0.72 57.67 ? C4' ADP 401 A 1 
HETATM 12 O O4' ADP . . . D 4 -6.65 44.54 -7.458 0.72 65.2 ? O4' ADP 401 A 1 
HETATM 13 C C3' ADP . . . D 4 -6.032 43.08 -9.268 0.72 59.55 ? C3' ADP 401 A 1 
HETATM 14 O O3' ADP . . . D 4 -5.117 43.089 -10.404 0.72 58.87 ? O3' ADP 401 A 1 
HETATM 15 C C2' ADP . . . D 4 -5.369 42.597 -8.072 0.72 59.25 ? C2' ADP 401 A 1 
HETATM 16 O O2' ADP . . . D 4 -3.942 42.888 -8.142 0.72 57.09 ? O2' ADP 401 A 1 
HETATM 17 C C1' ADP . . . D 4 -5.969 43.308 -6.929 0.72 62.29 ? C1' ADP 401 A 1 
HETATM 18 N N9 ADP . . . D 4 -6.863 42.447 -6.321 0.72 61.27 ? N9 ADP 401 A 1 
HETATM 19 C C8 ADP . . . D 4 -8.029 41.997 -6.796 0.72 60.99 ? C8 ADP 401 A 1 
HETATM 20 N N7 ADP . . . D 4 -8.58 41.174 -5.932 0.72 54.41 ? N7 ADP 401 A 1 
HETATM 21 C C5 ADP . . . D 4 -7.787 41.064 -4.878 0.72 52.03 ? C5 ADP 401 A 1 
HETATM 22 C C6 ADP . . . D 4 -7.846 40.36 -3.704 0.72 43.52 ? C6 ADP 401 A 1 
HETATM 23 N N6 ADP . . . D 4 -8.953 39.533 -3.435 0.72 46.63 ? N6 ADP 401 A 1 
HETATM 24 N N1 ADP . . . D 4 -6.855 40.464 -2.821 0.72 42.28 ? N1 ADP 401 A 1 
HETATM 25 C C2 ADP . . . D 4 -5.795 41.246 -3.047 0.72 42.83 ? C2 ADP 401 A 1 
HETATM 26 N N3 ADP . . . D 4 -5.696 41.945 -4.186 0.72 47.41 ? N3 ADP 401 A 1 
HETATM 27 C C4 ADP . . . D 4 -6.665 41.875 -5.107 0.72 54.97 ? C4 ADP 401 A 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           326 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           27 
#