data_3EQI
#
_model_server_result.job_id            K6JxG8ytqdn8oFaSAVkutA 
_model_server_result.datetime_utc      '2024-11-04 23:05:26' 
_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          3eqi 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":2}' 
#
_entry.id    3EQI 
#
_exptl.entry_id    3EQI 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          2 
_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            3EQI 
_cell.length_a            76.89 
_cell.length_b            76.89 
_cell.length_c            222.61 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3EQI 
_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
PQS monomeric 1 author_and_software_defined_assembly 1 
PISA dimeric 2 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 1 1 
A,B,C,D,E,F 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' 11_555 -x+y,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 111.305 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_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 O1B ADP . A ADP 2 1_555 C MG MG . A MG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? 
metalc ? metalc2 B O2A ADP . A ADP 2 1_555 C MG MG . A MG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? 
metalc ? metalc3 C MG MG . A MG 3 1_555 A OD1 ASN 162 A ASN 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? 
metalc ? metalc4 C MG MG . A MG 3 1_555 A OD2 ASP 175 A ASP 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc5 C MG MG . A MG 3 1_555 F O HOH . A HOH 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? 
metalc ? metalc6 C MG MG . A MG 3 1_555 F O HOH . A HOH 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
metalc ? metalc7 D CA CA . A CA 5 1_555 A OD1 ASP 32 A ASP 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 4.46 ? 
metalc ? metalc8 D CA CA . A CA 5 1_555 A OD2 ASP 32 A ASP 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? 
metalc ? metalc9 D CA CA . A CA 5 1_555 A OD1 ASP 33 A ASP 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? 
metalc ? metalc10 E NA NA . A NA 6 1_555 A OD1 ASP 32 A ASP 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? 
metalc ? metalc11 E NA NA . A NA 6 1_555 A OD2 ASP 32 A ASP 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? 
metalc ? metalc12 E NA NA . A NA 6 1_555 F O HOH . A HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? 
metalc ? metalc13 E NA NA . A NA 6 1_555 F O HOH . A HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? 
metalc ? metalc14 E NA NA . A NA 6 1_555 F O HOH . A HOH 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? 
#
_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                     3EQI 
_atom_sites.fract_transf_matrix[1][1]    0.013006 
_atom_sites.fract_transf_matrix[1][2]    0.007509 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015018 
_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]    0.004492 
_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
B 2 ADP A 1 2 2 ADP ADP . 
C 3 MG A 1 3 3 MG MG . 
D 4 CA A 1 5 5 CA CA . 
E 5 NA A 1 6 6 NA NA . 
F 6 HOH A 1 394 394 HOH HOH . 
F 6 HOH A 2 395 395 HOH HOH . 
F 6 HOH A 3 396 396 HOH HOH . 
F 6 HOH A 4 397 397 HOH HOH . 
F 6 HOH A 5 398 398 HOH HOH . 
F 6 HOH A 6 399 399 HOH HOH . 
F 6 HOH A 7 400 400 HOH HOH . 
F 6 HOH A 8 401 401 HOH HOH . 
F 6 HOH A 9 402 402 HOH HOH . 
F 6 HOH A 10 403 403 HOH HOH . 
F 6 HOH A 11 404 404 HOH HOH . 
F 6 HOH A 12 405 405 HOH HOH . 
F 6 HOH A 13 406 406 HOH HOH . 
F 6 HOH A 14 407 407 HOH HOH . 
F 6 HOH A 15 408 408 HOH HOH . 
F 6 HOH A 16 409 409 HOH HOH . 
F 6 HOH A 17 410 410 HOH HOH . 
F 6 HOH A 18 411 411 HOH HOH . 
F 6 HOH A 19 412 412 HOH HOH . 
F 6 HOH A 20 413 413 HOH HOH . 
F 6 HOH A 21 414 414 HOH HOH . 
F 6 HOH A 22 415 415 HOH HOH . 
F 6 HOH A 23 416 416 HOH HOH . 
F 6 HOH A 24 417 417 HOH HOH . 
F 6 HOH A 25 418 418 HOH HOH . 
F 6 HOH A 26 419 419 HOH HOH . 
F 6 HOH A 27 420 420 HOH HOH . 
F 6 HOH A 28 421 421 HOH HOH . 
F 6 HOH A 29 422 422 HOH HOH . 
F 6 HOH A 30 423 423 HOH HOH . 
F 6 HOH A 31 424 424 HOH HOH . 
F 6 HOH A 32 425 425 HOH HOH . 
F 6 HOH A 33 426 426 HOH HOH . 
F 6 HOH A 34 427 427 HOH HOH . 
F 6 HOH A 35 428 428 HOH HOH . 
F 6 HOH A 36 429 429 HOH HOH . 
F 6 HOH A 37 430 430 HOH HOH . 
F 6 HOH A 38 431 431 HOH HOH . 
F 6 HOH A 39 432 432 HOH HOH . 
F 6 HOH A 40 433 433 HOH HOH . 
F 6 HOH A 41 434 434 HOH HOH . 
F 6 HOH A 42 435 435 HOH HOH . 
F 6 HOH A 43 436 436 HOH HOH . 
F 6 HOH A 44 437 437 HOH HOH . 
F 6 HOH A 45 438 438 HOH HOH . 
F 6 HOH A 46 439 439 HOH HOH . 
F 6 HOH A 47 440 440 HOH HOH . 
F 6 HOH A 48 441 441 HOH HOH . 
F 6 HOH A 49 442 442 HOH HOH . 
F 6 HOH A 50 443 443 HOH HOH . 
F 6 HOH A 51 444 444 HOH HOH . 
F 6 HOH A 52 445 445 HOH HOH . 
F 6 HOH A 53 446 446 HOH HOH . 
F 6 HOH A 54 447 447 HOH HOH . 
F 6 HOH A 55 448 448 HOH HOH . 
F 6 HOH A 56 449 449 HOH HOH . 
F 6 HOH A 57 450 450 HOH HOH . 
F 6 HOH A 58 451 451 HOH HOH . 
F 6 HOH A 59 452 452 HOH HOH . 
F 6 HOH A 60 453 453 HOH HOH . 
F 6 HOH A 61 454 454 HOH HOH . 
F 6 HOH A 62 455 455 HOH HOH . 
F 6 HOH A 63 456 456 HOH HOH . 
F 6 HOH A 64 457 457 HOH HOH . 
F 6 HOH A 65 458 458 HOH HOH . 
F 6 HOH A 66 459 459 HOH HOH . 
F 6 HOH A 67 460 460 HOH HOH . 
F 6 HOH A 68 461 461 HOH HOH . 
F 6 HOH A 69 462 462 HOH HOH . 
F 6 HOH A 70 463 463 HOH HOH . 
F 6 HOH A 71 464 464 HOH HOH . 
F 6 HOH A 72 465 465 HOH HOH . 
F 6 HOH A 73 466 466 HOH HOH . 
F 6 HOH A 74 467 467 HOH HOH . 
F 6 HOH A 75 468 468 HOH HOH . 
F 6 HOH A 76 469 469 HOH HOH . 
F 6 HOH A 77 470 470 HOH HOH . 
F 6 HOH A 78 471 471 HOH HOH . 
F 6 HOH A 79 472 472 HOH HOH . 
F 6 HOH A 80 473 473 HOH HOH . 
F 6 HOH A 81 474 474 HOH HOH . 
F 6 HOH A 82 475 475 HOH HOH . 
F 6 HOH A 83 476 476 HOH HOH . 
F 6 HOH A 84 477 477 HOH HOH . 
F 6 HOH A 85 478 478 HOH HOH . 
F 6 HOH A 86 479 479 HOH HOH . 
F 6 HOH A 87 480 480 HOH HOH . 
F 6 HOH A 88 481 481 HOH HOH . 
F 6 HOH A 89 482 482 HOH HOH . 
F 6 HOH A 90 483 483 HOH HOH . 
F 6 HOH A 91 484 484 HOH HOH . 
F 6 HOH A 92 485 485 HOH HOH . 
F 6 HOH A 93 486 486 HOH HOH . 
F 6 HOH A 94 487 487 HOH HOH . 
F 6 HOH A 95 488 488 HOH HOH . 
F 6 HOH A 96 489 489 HOH HOH . 
F 6 HOH A 97 490 490 HOH HOH . 
F 6 HOH A 98 491 491 HOH HOH . 
F 6 HOH A 99 492 492 HOH HOH . 
F 6 HOH A 100 493 493 HOH HOH . 
F 6 HOH A 101 494 494 HOH HOH . 
F 6 HOH A 102 495 495 HOH HOH . 
F 6 HOH A 103 496 496 HOH HOH . 
F 6 HOH A 104 497 497 HOH HOH . 
F 6 HOH A 105 498 498 HOH HOH . 
F 6 HOH A 106 499 499 HOH HOH . 
F 6 HOH A 107 500 500 HOH HOH . 
F 6 HOH A 108 501 501 HOH HOH . 
F 6 HOH A 109 502 502 HOH HOH . 
F 6 HOH A 110 503 503 HOH HOH . 
F 6 HOH A 111 504 504 HOH HOH . 
F 6 HOH A 112 505 505 HOH HOH . 
F 6 HOH A 113 506 506 HOH HOH . 
F 6 HOH A 114 507 507 HOH HOH . 
F 6 HOH A 115 508 508 HOH HOH . 
F 6 HOH A 116 509 509 HOH HOH . 
F 6 HOH A 117 510 510 HOH HOH . 
F 6 HOH A 118 511 511 HOH HOH . 
F 6 HOH A 119 512 512 HOH HOH . 
F 6 HOH A 120 513 513 HOH HOH . 
F 6 HOH A 121 514 514 HOH HOH . 
F 6 HOH A 122 515 515 HOH HOH . 
F 6 HOH A 123 516 516 HOH HOH . 
F 6 HOH A 124 517 517 HOH HOH . 
F 6 HOH A 125 518 518 HOH HOH . 
F 6 HOH A 126 519 519 HOH HOH . 
F 6 HOH A 127 520 520 HOH HOH . 
F 6 HOH A 128 521 521 HOH HOH . 
F 6 HOH A 129 522 522 HOH HOH . 
F 6 HOH A 130 523 393 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 . . . B 2 -9.926 63.412 32.961 1 58.21 ? PB ADP 2 A 1 
HETATM 2 O O1B ADP . . . B 2 -8.737 63.325 32.029 1 56.49 ? O1B ADP 2 A 1 
HETATM 3 O O2B ADP . . . B 2 -10.651 64.703 32.694 1 58.4 ? O2B ADP 2 A 1 
HETATM 4 O O3B ADP . . . B 2 -10.889 62.159 32.812 1 59.2 ? O3B ADP 2 A 1 
HETATM 5 P PA ADP . . . B 2 -8.077 63.739 35.176 1 56.97 ? PA ADP 2 A 1 
HETATM 6 O O1A ADP . . . B 2 -8.034 63.404 36.644 1 58.28 ? O1A ADP 2 A 1 
HETATM 7 O O2A ADP . . . B 2 -6.879 63.113 34.541 1 55.72 ? O2A ADP 2 A 1 
HETATM 8 O O3A ADP . . . B 2 -9.464 63.388 34.503 1 58.08 ? O3A ADP 2 A 1 
HETATM 9 O O5' ADP . . . B 2 -7.956 65.307 35.008 1 53.36 ? O5' ADP 2 A 1 
HETATM 10 C C5' ADP . . . B 2 -9.118 66.126 35.303 1 51.07 ? C5' ADP 2 A 1 
HETATM 11 C C4' ADP . . . B 2 -8.87 67.496 34.674 1 48.79 ? C4' ADP 2 A 1 
HETATM 12 O O4' ADP . . . B 2 -7.757 68.17 35.316 1 44.91 ? O4' ADP 2 A 1 
HETATM 13 C C3' ADP . . . B 2 -8.447 67.498 33.215 1 50.36 ? C3' ADP 2 A 1 
HETATM 14 O O3' ADP . . . B 2 -9.583 67.231 32.393 1 53.47 ? O3' ADP 2 A 1 
HETATM 15 C C2' ADP . . . B 2 -7.811 68.893 33.107 1 47 ? C2' ADP 2 A 1 
HETATM 16 O O2' ADP . . . B 2 -8.822 69.875 32.952 1 48.35 ? O2' ADP 2 A 1 
HETATM 17 C C1' ADP . . . B 2 -7.173 69.127 34.486 1 43.95 ? C1' ADP 2 A 1 
HETATM 18 N N9 ADP . . . B 2 -5.709 68.962 34.509 1 39.87 ? N9 ADP 2 A 1 
HETATM 19 C C8 ADP . . . B 2 -4.992 67.799 34.605 1 39.06 ? C8 ADP 2 A 1 
HETATM 20 N N7 ADP . . . B 2 -3.643 67.984 34.557 1 37.79 ? N7 ADP 2 A 1 
HETATM 21 C C5 ADP . . . B 2 -3.474 69.36 34.434 1 35.68 ? C5 ADP 2 A 1 
HETATM 22 C C6 ADP . . . B 2 -2.301 70.143 34.357 1 34.57 ? C6 ADP 2 A 1 
HETATM 23 N N6 ADP . . . B 2 -1.077 69.787 34.367 1 34.43 ? N6 ADP 2 A 1 
HETATM 24 N N1 ADP . . . B 2 -2.621 71.475 34.246 1 33.59 ? N1 ADP 2 A 1 
HETATM 25 C C2 ADP . . . B 2 -3.885 72.024 34.202 1 36.09 ? C2 ADP 2 A 1 
HETATM 26 N N3 ADP . . . B 2 -4.984 71.305 34.275 1 37.31 ? N3 ADP 2 A 1 
HETATM 27 C C4 ADP . . . B 2 -4.746 69.976 34.396 1 37.48 ? C4 ADP 2 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           273 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           27 
#