data_3RTD
#
_model_server_result.job_id            7tlCML6jKkYHrTAxKOnQMA 
_model_server_result.datetime_utc      '2024-11-22 08:35:46' 
_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          3rtd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":494}' 
#
_entry.id    3RTD 
#
_exptl.entry_id    3RTD 
_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         90 
_cell.entry_id            3RTD 
_cell.length_a            121.81 
_cell.length_b            121.81 
_cell.length_c            155.221 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3RTD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        97 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 4 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexadecameric 
_pdbx_struct_assembly.oligomeric_count      16 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4,5,6,7,8 
#
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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 
3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 
4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 
5 'crystal symmetry operation' 5_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 
6 'crystal symmetry operation' 6_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 
7 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 
8 'crystal symmetry operation' 8_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      6 
_struct_asym.id                             F 
_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 64 A ASN 52 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.781 ? 
metalc ? metalc2 A O ASP 126 A ASP 114 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.873 ? 
metalc ? metalc3 A OD2 ASP 126 A ASP 114 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.466 ? 
metalc ? metalc4 A O PHE 129 A PHE 117 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.692 ? 
metalc ? metalc5 A O VAL 158 A VAL 146 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.87 ? 
metalc ? metalc6 A O VAL 160 A VAL 148 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.736 ? 
metalc ? metalc7 A OG SER 162 A SER 150 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.919 ? 
metalc ? metalc8 D MG MG . A MG 492 1_555 F O1A ADP . A ADP 494 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? 
metalc ? metalc9 D MG MG . A MG 492 1_555 F O1B ADP . A ADP 494 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? 
metalc ? metalc10 D MG MG . A MG 492 1_555 H O HOH . A HOH 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? 
metalc ? metalc11 D MG MG . A MG 492 1_555 H O HOH . A HOH 527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? 
metalc ? metalc12 D MG MG . A MG 492 1_555 H O HOH . A HOH 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? 
#
_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                     3RTD 
_atom_sites.fract_transf_matrix[1][1]    0.00821 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00821 
_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]    0.006442 
_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 K A 1 491 491 K K . 
D 4 MG A 1 492 492 MG MG . 
E 5 NAI A 1 493 493 NAI NAI . 
F 6 ADP A 1 494 494 ADP ADP . 
G 7 NAX A 1 495 495 NAX NAX . 
H 8 HOH A 1 496 496 HOH HOH . 
H 8 HOH A 2 497 497 HOH HOH . 
H 8 HOH A 3 498 498 HOH HOH . 
H 8 HOH A 4 499 499 HOH HOH . 
H 8 HOH A 5 500 500 HOH HOH . 
H 8 HOH A 6 501 501 HOH HOH . 
H 8 HOH A 7 502 502 HOH HOH . 
H 8 HOH A 8 503 503 HOH HOH . 
H 8 HOH A 9 504 504 HOH HOH . 
H 8 HOH A 10 505 505 HOH HOH . 
H 8 HOH A 11 506 506 HOH HOH . 
H 8 HOH A 12 507 507 HOH HOH . 
H 8 HOH A 13 508 508 HOH HOH . 
H 8 HOH A 14 509 509 HOH HOH . 
H 8 HOH A 15 510 510 HOH HOH . 
H 8 HOH A 16 511 511 HOH HOH . 
H 8 HOH A 17 512 512 HOH HOH . 
H 8 HOH A 18 513 513 HOH HOH . 
H 8 HOH A 19 514 514 HOH HOH . 
H 8 HOH A 20 515 515 HOH HOH . 
H 8 HOH A 21 516 516 HOH HOH . 
H 8 HOH A 22 517 517 HOH HOH . 
H 8 HOH A 23 518 518 HOH HOH . 
H 8 HOH A 24 519 519 HOH HOH . 
H 8 HOH A 25 520 520 HOH HOH . 
H 8 HOH A 26 521 521 HOH HOH . 
H 8 HOH A 27 522 522 HOH HOH . 
H 8 HOH A 28 523 523 HOH HOH . 
H 8 HOH A 29 524 524 HOH HOH . 
H 8 HOH A 30 525 525 HOH HOH . 
H 8 HOH A 31 526 526 HOH HOH . 
H 8 HOH A 32 527 527 HOH HOH . 
H 8 HOH A 33 528 528 HOH HOH . 
H 8 HOH A 34 529 529 HOH HOH . 
H 8 HOH A 35 530 530 HOH HOH . 
H 8 HOH A 36 531 531 HOH HOH . 
H 8 HOH A 37 532 532 HOH HOH . 
H 8 HOH A 38 533 533 HOH HOH . 
H 8 HOH A 39 534 534 HOH HOH . 
H 8 HOH A 40 535 535 HOH HOH . 
H 8 HOH A 41 536 536 HOH HOH . 
H 8 HOH A 42 537 537 HOH HOH . 
H 8 HOH A 43 538 538 HOH HOH . 
H 8 HOH A 44 539 539 HOH HOH . 
H 8 HOH A 45 540 540 HOH HOH . 
H 8 HOH A 46 541 541 HOH HOH . 
H 8 HOH A 47 542 542 HOH HOH . 
H 8 HOH A 48 543 543 HOH HOH . 
H 8 HOH A 49 544 544 HOH HOH . 
H 8 HOH A 50 545 545 HOH HOH . 
H 8 HOH A 51 546 546 HOH HOH . 
H 8 HOH A 52 547 547 HOH HOH . 
H 8 HOH A 53 548 548 HOH HOH . 
H 8 HOH A 54 549 549 HOH HOH . 
H 8 HOH A 55 550 550 HOH HOH . 
H 8 HOH A 56 551 551 HOH HOH . 
H 8 HOH A 57 552 552 HOH HOH . 
H 8 HOH A 58 553 553 HOH HOH . 
H 8 HOH A 59 554 554 HOH HOH . 
H 8 HOH A 60 555 555 HOH HOH . 
H 8 HOH A 61 556 556 HOH HOH . 
H 8 HOH A 62 557 557 HOH HOH . 
H 8 HOH A 63 558 558 HOH HOH . 
H 8 HOH A 64 559 559 HOH HOH . 
H 8 HOH A 65 560 560 HOH HOH . 
H 8 HOH A 66 561 561 HOH HOH . 
H 8 HOH A 67 562 562 HOH HOH . 
H 8 HOH A 68 563 563 HOH HOH . 
H 8 HOH A 69 564 564 HOH HOH . 
H 8 HOH A 70 565 565 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 . . . F 6 -5.235 21.068 41.398 1 36.7 ? PB ADP 494 A 1 
HETATM 2 O O1B ADP . . . F 6 -4.803 21.497 42.813 1 32.54 ? O1B ADP 494 A 1 
HETATM 3 O O2B ADP . . . F 6 -4.197 20.184 40.88 1 35.02 ? O2B ADP 494 A 1 
HETATM 4 O O3B ADP . . . F 6 -6.626 20.602 41.238 1 34.88 ? O3B ADP 494 A 1 
HETATM 5 P PA ADP . . . F 6 -4.803 23.725 40.245 1 34.77 ? PA ADP 494 A 1 
HETATM 6 O O1A ADP . . . F 6 -3.695 24.049 41.205 1 35.78 ? O1A ADP 494 A 1 
HETATM 7 O O2A ADP . . . F 6 -5.952 24.595 39.9 1 42.24 ? O2A ADP 494 A 1 
HETATM 8 O O3A ADP . . . F 6 -5.595 22.372 40.518 1 35.85 ? O3A ADP 494 A 1 
HETATM 9 O O5' ADP . . . F 6 -4.1 23.584 38.792 1 35.55 ? O5' ADP 494 A 1 
HETATM 10 C C5' ADP . . . F 6 -4.875 23.327 37.607 1 27.02 ? C5' ADP 494 A 1 
HETATM 11 C C4' ADP . . . F 6 -3.889 23.189 36.459 1 29.81 ? C4' ADP 494 A 1 
HETATM 12 O O4' ADP . . . F 6 -4.602 22.787 35.292 1 29.54 ? O4' ADP 494 A 1 
HETATM 13 C C3' ADP . . . F 6 -3.261 24.541 36.096 1 31.39 ? C3' ADP 494 A 1 
HETATM 14 O O3' ADP . . . F 6 -2.043 24.4 35.422 1 32.9 ? O3' ADP 494 A 1 
HETATM 15 C C2' ADP . . . F 6 -4.254 25.139 35.137 1 31.85 ? C2' ADP 494 A 1 
HETATM 16 O O2' ADP . . . F 6 -3.764 26.283 34.449 1 33.93 ? O2' ADP 494 A 1 
HETATM 17 C C1' ADP . . . F 6 -4.592 23.879 34.347 1 31.7 ? C1' ADP 494 A 1 
HETATM 18 N N9 ADP . . . F 6 -5.966 23.938 33.796 1 34.16 ? N9 ADP 494 A 1 
HETATM 19 C C8 ADP . . . F 6 -7.126 23.749 34.461 1 31.14 ? C8 ADP 494 A 1 
HETATM 20 N N7 ADP . . . F 6 -8.177 23.868 33.611 1 29.88 ? N7 ADP 494 A 1 
HETATM 21 C C5 ADP . . . F 6 -7.671 24.156 32.408 1 28.61 ? C5 ADP 494 A 1 
HETATM 22 C C6 ADP . . . F 6 -8.22 24.444 31.081 1 29.79 ? C6 ADP 494 A 1 
HETATM 23 N N6 ADP . . . F 6 -9.553 24.43 30.873 1 32.29 ? N6 ADP 494 A 1 
HETATM 24 N N1 ADP . . . F 6 -7.367 24.695 30.086 1 31.19 ? N1 ADP 494 A 1 
HETATM 25 C C2 ADP . . . F 6 -6.034 24.715 30.247 1 28.76 ? C2 ADP 494 A 1 
HETATM 26 N N3 ADP . . . F 6 -5.46 24.514 31.447 1 34.54 ? N3 ADP 494 A 1 
HETATM 27 C C4 ADP . . . F 6 -6.229 24.192 32.526 1 31.48 ? C4 ADP 494 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           345 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           27 
#