data_4NM5
#
_model_server_result.job_id            --se19qGiqh39xZEX5zxVw 
_model_server_result.datetime_utc      '2024-10-11 00:33:03' 
_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          4nm5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":401}' 
#
_entry.id    4NM5 
#
_exptl.entry_id    4NM5 
_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            4NM5 
_cell.length_a            81.727 
_cell.length_b            81.727 
_cell.length_c            280.937 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4NM5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61 2 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA trimeric 3 author_and_software_defined_assembly 1 
PISA hexameric 6 software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H,I,J,K,L,M 1 1 
A,B,C,D,E,F,G,H,I,J,K,L,M 2 1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 10_664 -y+1,-x+1,-z-1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 40.8635 70.777658 -46.822833 
#
_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 1571 1_555 C N TPO 6 C TPO 1572 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale2 C C TPO 6 C TPO 1572 1_555 C N PRO 7 C PRO 1573 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? 
metalc ? metalc1 A OD1 ASN 174 A ASN 186 1_555 I MG MG . A MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 
metalc ? metalc2 A OD2 ASP 188 A ASP 200 1_555 I MG MG . A MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? 
metalc ? metalc3 A OD1 ASP 188 A ASP 200 1_555 J MG MG . A MG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? 
metalc ? metalc4 D O1A ADP . A ADP 401 1_555 I MG MG . A MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? 
metalc ? metalc5 D O1B ADP . A ADP 401 1_555 I MG MG . A MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? 
metalc ? metalc6 D O2B ADP . A ADP 401 1_555 J MG MG . A MG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? 
metalc ? metalc7 I MG MG . A MG 406 1_555 L O HOH . A HOH 572 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? 
#
_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                     4NM5 
_atom_sites.fract_transf_matrix[1][1]    0.012236 
_atom_sites.fract_transf_matrix[1][2]    0.007064 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014129 
_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]    0.00356 
_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 3 GOL GOL . 
H 5 GOL A 1 405 4 GOL GOL . 
I 6 MG A 1 406 1 MG MG . 
J 6 MG A 1 407 2 MG MG . 
K 7 CL A 1 408 1 CL CL . 
L 8 HOH A 1 501 1 HOH HOH . 
L 8 HOH A 2 502 2 HOH HOH . 
L 8 HOH A 3 503 3 HOH HOH . 
L 8 HOH A 4 504 4 HOH HOH . 
L 8 HOH A 5 505 5 HOH HOH . 
L 8 HOH A 6 506 6 HOH HOH . 
L 8 HOH A 7 507 7 HOH HOH . 
L 8 HOH A 8 508 8 HOH HOH . 
L 8 HOH A 9 509 9 HOH HOH . 
L 8 HOH A 10 510 10 HOH HOH . 
L 8 HOH A 11 511 11 HOH HOH . 
L 8 HOH A 12 512 12 HOH HOH . 
L 8 HOH A 13 513 13 HOH HOH . 
L 8 HOH A 14 514 14 HOH HOH . 
L 8 HOH A 15 515 15 HOH HOH . 
L 8 HOH A 16 516 16 HOH HOH . 
L 8 HOH A 17 517 17 HOH HOH . 
L 8 HOH A 18 518 18 HOH HOH . 
L 8 HOH A 19 519 19 HOH HOH . 
L 8 HOH A 20 520 20 HOH HOH . 
L 8 HOH A 21 521 21 HOH HOH . 
L 8 HOH A 22 522 22 HOH HOH . 
L 8 HOH A 23 523 23 HOH HOH . 
L 8 HOH A 24 524 24 HOH HOH . 
L 8 HOH A 25 525 25 HOH HOH . 
L 8 HOH A 26 526 26 HOH HOH . 
L 8 HOH A 27 527 27 HOH HOH . 
L 8 HOH A 28 528 28 HOH HOH . 
L 8 HOH A 29 529 29 HOH HOH . 
L 8 HOH A 30 530 30 HOH HOH . 
L 8 HOH A 31 531 31 HOH HOH . 
L 8 HOH A 32 532 32 HOH HOH . 
L 8 HOH A 33 533 33 HOH HOH . 
L 8 HOH A 34 534 34 HOH HOH . 
L 8 HOH A 35 535 35 HOH HOH . 
L 8 HOH A 36 536 36 HOH HOH . 
L 8 HOH A 37 537 37 HOH HOH . 
L 8 HOH A 38 538 38 HOH HOH . 
L 8 HOH A 39 539 39 HOH HOH . 
L 8 HOH A 40 540 40 HOH HOH . 
L 8 HOH A 41 541 41 HOH HOH . 
L 8 HOH A 42 542 43 HOH HOH . 
L 8 HOH A 43 543 44 HOH HOH . 
L 8 HOH A 44 544 45 HOH HOH . 
L 8 HOH A 45 545 46 HOH HOH . 
L 8 HOH A 46 546 47 HOH HOH . 
L 8 HOH A 47 547 48 HOH HOH . 
L 8 HOH A 48 548 49 HOH HOH . 
L 8 HOH A 49 549 50 HOH HOH . 
L 8 HOH A 50 550 51 HOH HOH . 
L 8 HOH A 51 551 53 HOH HOH . 
L 8 HOH A 52 552 54 HOH HOH . 
L 8 HOH A 53 553 55 HOH HOH . 
L 8 HOH A 54 554 56 HOH HOH . 
L 8 HOH A 55 555 58 HOH HOH . 
L 8 HOH A 56 556 59 HOH HOH . 
L 8 HOH A 57 557 60 HOH HOH . 
L 8 HOH A 58 558 61 HOH HOH . 
L 8 HOH A 59 559 62 HOH HOH . 
L 8 HOH A 60 560 63 HOH HOH . 
L 8 HOH A 61 561 64 HOH HOH . 
L 8 HOH A 62 562 65 HOH HOH . 
L 8 HOH A 63 563 67 HOH HOH . 
L 8 HOH A 64 564 68 HOH HOH . 
L 8 HOH A 65 565 69 HOH HOH . 
L 8 HOH A 66 566 71 HOH HOH . 
L 8 HOH A 67 567 72 HOH HOH . 
L 8 HOH A 68 568 73 HOH HOH . 
L 8 HOH A 69 569 74 HOH HOH . 
L 8 HOH A 70 570 75 HOH HOH . 
L 8 HOH A 71 571 77 HOH HOH . 
L 8 HOH A 72 572 78 HOH HOH . 
L 8 HOH A 73 573 80 HOH HOH . 
L 8 HOH A 74 574 81 HOH HOH . 
L 8 HOH A 75 575 82 HOH HOH . 
L 8 HOH A 76 576 83 HOH HOH . 
L 8 HOH A 77 577 84 HOH HOH . 
L 8 HOH A 78 578 85 HOH HOH . 
L 8 HOH A 79 579 86 HOH HOH . 
L 8 HOH A 80 580 87 HOH HOH . 
L 8 HOH A 81 581 88 HOH HOH . 
L 8 HOH A 82 582 89 HOH HOH . 
L 8 HOH A 83 583 90 HOH HOH . 
L 8 HOH A 84 584 91 HOH HOH . 
L 8 HOH A 85 585 92 HOH HOH . 
L 8 HOH A 86 586 93 HOH HOH . 
L 8 HOH A 87 587 94 HOH HOH . 
L 8 HOH A 88 588 95 HOH HOH . 
L 8 HOH A 89 589 96 HOH HOH . 
L 8 HOH A 90 590 97 HOH HOH . 
L 8 HOH A 91 591 98 HOH HOH . 
L 8 HOH A 92 592 99 HOH HOH . 
L 8 HOH A 93 593 100 HOH HOH . 
L 8 HOH A 94 594 101 HOH HOH . 
L 8 HOH A 95 595 102 HOH HOH . 
L 8 HOH A 96 596 104 HOH HOH . 
L 8 HOH A 97 597 105 HOH HOH . 
L 8 HOH A 98 598 107 HOH HOH . 
L 8 HOH A 99 599 109 HOH HOH . 
L 8 HOH A 100 600 110 HOH HOH . 
L 8 HOH A 101 601 111 HOH HOH . 
L 8 HOH A 102 602 112 HOH HOH . 
L 8 HOH A 103 603 113 HOH HOH . 
L 8 HOH A 104 604 114 HOH HOH . 
L 8 HOH A 105 605 115 HOH HOH . 
L 8 HOH A 106 606 116 HOH HOH . 
L 8 HOH A 107 607 117 HOH HOH . 
L 8 HOH A 108 608 118 HOH HOH . 
L 8 HOH A 109 609 119 HOH HOH . 
L 8 HOH A 110 610 120 HOH HOH . 
L 8 HOH A 111 611 121 HOH HOH . 
M 8 HOH B 1 501 42 HOH HOH . 
M 8 HOH B 2 502 52 HOH HOH . 
M 8 HOH B 3 503 57 HOH HOH . 
M 8 HOH B 4 504 66 HOH HOH . 
M 8 HOH B 5 505 70 HOH HOH . 
M 8 HOH B 6 506 76 HOH HOH . 
M 8 HOH B 7 507 79 HOH HOH . 
M 8 HOH B 8 508 103 HOH HOH . 
M 8 HOH B 9 509 106 HOH HOH . 
M 8 HOH B 10 510 108 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 -10.76 44.931 -12.503 0.71 84.5 ? PB ADP 401 A 1 
HETATM 2 O O1B ADP . . . D 4 -9.688 44.403 -13.429 0.71 85.73 ? O1B ADP 401 A 1 
HETATM 3 O O2B ADP . . . D 4 -12.091 44.297 -12.82 0.71 91.15 ? O2B ADP 401 A 1 
HETATM 4 O O3B ADP . . . D 4 -10.88 46.424 -12.698 0.71 85.6 ? O3B ADP 401 A 1 
HETATM 5 P PA ADP . . . D 4 -9.82 43.271 -10.426 0.71 71.62 ? PA ADP 401 A 1 
HETATM 6 O O1A ADP . . . D 4 -9.03 42.536 -11.485 0.71 76.35 ? O1A ADP 401 A 1 
HETATM 7 O O2A ADP . . . D 4 -10.931 42.39 -9.9 0.71 53.74 ? O2A ADP 401 A 1 
HETATM 8 O O3A ADP . . . D 4 -10.387 44.635 -10.999 0.71 109.32 ? O3A ADP 401 A 1 
HETATM 9 O O5' ADP . . . D 4 -8.842 43.654 -9.252 0.71 78.39 ? O5' ADP 401 A 1 
HETATM 10 C C5' ADP . . . D 4 -7.968 44.725 -9.504 0.71 76.02 ? C5' ADP 401 A 1 
HETATM 11 C C4' ADP . . . D 4 -6.649 44.426 -8.932 0.71 77.25 ? C4' ADP 401 A 1 
HETATM 12 O O4' ADP . . . D 4 -6.764 44.423 -7.433 0.71 84.51 ? O4' ADP 401 A 1 
HETATM 13 C C3' ADP . . . D 4 -6.21 43.092 -9.363 0.71 76.15 ? C3' ADP 401 A 1 
HETATM 14 O O3' ADP . . . D 4 -5.265 43.194 -10.469 0.71 71.52 ? O3' ADP 401 A 1 
HETATM 15 C C2' ADP . . . D 4 -5.56 42.479 -8.225 0.71 78.53 ? C2' ADP 401 A 1 
HETATM 16 O O2' ADP . . . D 4 -4.12 42.679 -8.322 0.71 76.3 ? O2' ADP 401 A 1 
HETATM 17 C C1' ADP . . . D 4 -6.063 43.161 -7.02 0.71 82.03 ? C1' ADP 401 A 1 
HETATM 18 N N9 ADP . . . D 4 -6.968 42.331 -6.394 0.71 76.48 ? N9 ADP 401 A 1 
HETATM 19 C C8 ADP . . . D 4 -8.16 41.922 -6.839 0.71 74.2 ? C8 ADP 401 A 1 
HETATM 20 N N7 ADP . . . D 4 -8.719 41.127 -5.957 0.71 64.24 ? N7 ADP 401 A 1 
HETATM 21 C C5 ADP . . . D 4 -7.907 40.999 -4.92 0.71 62.3 ? C5 ADP 401 A 1 
HETATM 22 C C6 ADP . . . D 4 -7.966 40.309 -3.738 0.71 50.52 ? C6 ADP 401 A 1 
HETATM 23 N N6 ADP . . . D 4 -9.099 39.526 -3.444 0.71 55.99 ? N6 ADP 401 A 1 
HETATM 24 N N1 ADP . . . D 4 -6.953 40.387 -2.869 0.71 44.44 ? N1 ADP 401 A 1 
HETATM 25 C C2 ADP . . . D 4 -5.866 41.13 -3.125 0.71 46.43 ? C2 ADP 401 A 1 
HETATM 26 N N3 ADP . . . D 4 -5.771 41.818 -4.278 0.71 51.11 ? N3 ADP 401 A 1 
HETATM 27 C C4 ADP . . . D 4 -6.764 41.77 -5.179 0.71 64.64 ? C4 ADP 401 A 1 
#
_model_server_stats.io_time_ms              29 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           318 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#