data_6N4M
#
_model_server_result.job_id            KrVmk-r3NURk4hW686xvfA 
_model_server_result.datetime_utc      '2024-11-17 10:57:17' 
_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          6n4m 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":301}' 
#
_entry.id    6N4M 
#
_exptl.entry_id    6N4M 
_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         90 
_cell.entry_id            6N4M 
_cell.length_a            45.806 
_cell.length_b            74.579 
_cell.length_c            75.02 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6N4M 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 2 21 21' 
#
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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' 2_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 
#
_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 A OG SER 16 A SER 16 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? 
metalc ? metalc2 A SG CYS 97 A CYS 97 1_555 D FE1 SF4 . A SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? 
metalc ? metalc3 A SG CYS 132 A CYS 132 1_555 D FE2 SF4 . A SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 
metalc ? metalc4 B O3B ADP . A ADP 301 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
metalc ? metalc5 C MG MG . A MG 302 1_555 E O HOH . A HOH 416 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
metalc ? metalc6 C MG MG . A MG 302 1_555 E O HOH . A HOH 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? 
metalc ? metalc7 C MG MG . A MG 302 1_555 E O HOH . A HOH 441 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? 
metalc ? metalc8 C MG MG . A MG 302 1_555 E O HOH . A HOH 446 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? 
#
_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                     6N4M 
_atom_sites.fract_transf_matrix[1][1]    0.021831 
_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]    0.013409 
_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]    0.01333 
_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 1 301 1 ADP ADP . 
C 3 MG A 1 302 1 MG MG . 
D 4 SF4 A 1 303 2 SF4 FES . 
E 5 HOH A 1 401 93 HOH HOH . 
E 5 HOH A 2 402 63 HOH HOH . 
E 5 HOH A 3 403 85 HOH HOH . 
E 5 HOH A 4 404 78 HOH HOH . 
E 5 HOH A 5 405 19 HOH HOH . 
E 5 HOH A 6 406 95 HOH HOH . 
E 5 HOH A 7 407 55 HOH HOH . 
E 5 HOH A 8 408 45 HOH HOH . 
E 5 HOH A 9 409 105 HOH HOH . 
E 5 HOH A 10 410 49 HOH HOH . 
E 5 HOH A 11 411 13 HOH HOH . 
E 5 HOH A 12 412 70 HOH HOH . 
E 5 HOH A 13 413 87 HOH HOH . 
E 5 HOH A 14 414 103 HOH HOH . 
E 5 HOH A 15 415 39 HOH HOH . 
E 5 HOH A 16 416 15 HOH HOH . 
E 5 HOH A 17 417 29 HOH HOH . 
E 5 HOH A 18 418 27 HOH HOH . 
E 5 HOH A 19 419 3 HOH HOH . 
E 5 HOH A 20 420 40 HOH HOH . 
E 5 HOH A 21 421 75 HOH HOH . 
E 5 HOH A 22 422 1 HOH HOH . 
E 5 HOH A 23 423 99 HOH HOH . 
E 5 HOH A 24 424 30 HOH HOH . 
E 5 HOH A 25 425 22 HOH HOH . 
E 5 HOH A 26 426 2 HOH HOH . 
E 5 HOH A 27 427 4 HOH HOH . 
E 5 HOH A 28 428 88 HOH HOH . 
E 5 HOH A 29 429 118 HOH HOH . 
E 5 HOH A 30 430 56 HOH HOH . 
E 5 HOH A 31 431 14 HOH HOH . 
E 5 HOH A 32 432 51 HOH HOH . 
E 5 HOH A 33 433 34 HOH HOH . 
E 5 HOH A 34 434 48 HOH HOH . 
E 5 HOH A 35 435 26 HOH HOH . 
E 5 HOH A 36 436 77 HOH HOH . 
E 5 HOH A 37 437 74 HOH HOH . 
E 5 HOH A 38 438 18 HOH HOH . 
E 5 HOH A 39 439 8 HOH HOH . 
E 5 HOH A 40 440 97 HOH HOH . 
E 5 HOH A 41 441 9 HOH HOH . 
E 5 HOH A 42 442 16 HOH HOH . 
E 5 HOH A 43 443 17 HOH HOH . 
E 5 HOH A 44 444 20 HOH HOH . 
E 5 HOH A 45 445 73 HOH HOH . 
E 5 HOH A 46 446 11 HOH HOH . 
E 5 HOH A 47 447 67 HOH HOH . 
E 5 HOH A 48 448 50 HOH HOH . 
E 5 HOH A 49 449 47 HOH HOH . 
E 5 HOH A 50 450 36 HOH HOH . 
E 5 HOH A 51 451 57 HOH HOH . 
E 5 HOH A 52 452 42 HOH HOH . 
E 5 HOH A 53 453 7 HOH HOH . 
E 5 HOH A 54 454 5 HOH HOH . 
E 5 HOH A 55 455 12 HOH HOH . 
E 5 HOH A 56 456 117 HOH HOH . 
E 5 HOH A 57 457 112 HOH HOH . 
E 5 HOH A 58 458 32 HOH HOH . 
E 5 HOH A 59 459 43 HOH HOH . 
E 5 HOH A 60 460 72 HOH HOH . 
E 5 HOH A 61 461 38 HOH HOH . 
E 5 HOH A 62 462 76 HOH HOH . 
E 5 HOH A 63 463 66 HOH HOH . 
E 5 HOH A 64 464 101 HOH HOH . 
E 5 HOH A 65 465 59 HOH HOH . 
E 5 HOH A 66 466 79 HOH HOH . 
E 5 HOH A 67 467 113 HOH HOH . 
E 5 HOH A 68 468 116 HOH HOH . 
E 5 HOH A 69 469 21 HOH HOH . 
E 5 HOH A 70 470 98 HOH HOH . 
E 5 HOH A 71 471 6 HOH HOH . 
E 5 HOH A 72 472 114 HOH HOH . 
E 5 HOH A 73 473 37 HOH HOH . 
E 5 HOH A 74 474 35 HOH HOH . 
E 5 HOH A 75 475 23 HOH HOH . 
E 5 HOH A 76 476 28 HOH HOH . 
E 5 HOH A 77 477 24 HOH HOH . 
E 5 HOH A 78 478 53 HOH HOH . 
E 5 HOH A 79 479 86 HOH HOH . 
E 5 HOH A 80 480 81 HOH HOH . 
E 5 HOH A 81 482 54 HOH HOH . 
E 5 HOH A 82 483 96 HOH HOH . 
E 5 HOH A 83 484 41 HOH HOH . 
E 5 HOH A 84 485 62 HOH HOH . 
E 5 HOH A 85 486 44 HOH HOH . 
E 5 HOH A 86 487 119 HOH HOH . 
E 5 HOH A 87 488 91 HOH HOH . 
E 5 HOH A 88 489 33 HOH HOH . 
E 5 HOH A 89 490 109 HOH HOH . 
E 5 HOH A 90 491 71 HOH HOH . 
E 5 HOH A 91 492 100 HOH HOH . 
E 5 HOH A 92 493 108 HOH HOH . 
E 5 HOH A 93 494 89 HOH HOH . 
E 5 HOH A 94 495 52 HOH HOH . 
E 5 HOH A 95 496 25 HOH HOH . 
E 5 HOH A 96 497 68 HOH HOH . 
E 5 HOH A 97 498 31 HOH HOH . 
E 5 HOH A 98 499 120 HOH HOH . 
E 5 HOH A 99 500 104 HOH HOH . 
E 5 HOH A 100 501 10 HOH HOH . 
E 5 HOH A 101 502 82 HOH HOH . 
E 5 HOH A 102 503 115 HOH HOH . 
E 5 HOH A 103 504 102 HOH HOH . 
E 5 HOH A 104 505 58 HOH HOH . 
E 5 HOH A 105 506 46 HOH HOH . 
E 5 HOH A 106 507 84 HOH HOH . 
E 5 HOH A 107 508 107 HOH HOH . 
E 5 HOH A 108 509 121 HOH HOH . 
E 5 HOH A 109 510 61 HOH HOH . 
E 5 HOH A 110 511 122 HOH HOH . 
E 5 HOH A 111 512 94 HOH HOH . 
E 5 HOH A 112 513 64 HOH HOH . 
E 5 HOH A 113 514 65 HOH HOH . 
E 5 HOH A 114 515 60 HOH HOH . 
E 5 HOH A 115 516 111 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 4.422 -1.632 8.253 1 15.88 ? PB ADP 301 A 1 
HETATM 2 O O1B ADP . . . B 2 3.917 -2.489 7.123 1 16.18 ? O1B ADP 301 A 1 
HETATM 3 O O2B ADP . . . B 2 4.399 -0.144 7.952 1 14.91 ? O2B ADP 301 A 1 
HETATM 4 O O3B ADP . . . B 2 3.808 -1.988 9.574 1 14.72 ? O3B ADP 301 A 1 
HETATM 5 P PA ADP . . . B 2 6.785 -2.725 9.561 1 16.8 ? PA ADP 301 A 1 
HETATM 6 O O1A ADP . . . B 2 6.26 -4.132 9.646 1 16.09 ? O1A ADP 301 A 1 
HETATM 7 O O2A ADP . . . B 2 6.773 -1.937 10.824 1 16.56 ? O2A ADP 301 A 1 
HETATM 8 O O3A ADP . . . B 2 5.999 -1.958 8.39 1 15.3 ? O3A ADP 301 A 1 
HETATM 9 O O5' ADP . . . B 2 8.286 -2.708 8.998 1 16.73 ? O5' ADP 301 A 1 
HETATM 10 C C5' ADP . . . B 2 8.597 -3.405 7.769 1 16.97 ? C5' ADP 301 A 1 
HETATM 11 C C4' ADP . . . B 2 9.941 -4.08 7.892 1 20.51 ? C4' ADP 301 A 1 
HETATM 12 O O4' ADP . . . B 2 10.965 -3.072 8.084 1 19.17 ? O4' ADP 301 A 1 
HETATM 13 C C3' ADP . . . B 2 10.112 -5.083 9.043 1 22.88 ? C3' ADP 301 A 1 
HETATM 14 O O3' ADP . . . B 2 10.95 -6.173 8.664 1 29.95 ? O3' ADP 301 A 1 
HETATM 15 C C2' ADP . . . B 2 10.818 -4.25 10.109 1 21.64 ? C2' ADP 301 A 1 
HETATM 16 O O2' ADP . . . B 2 11.609 -5.002 11 1 24.98 ? O2' ADP 301 A 1 
HETATM 17 C C1' ADP . . . B 2 11.714 -3.373 9.242 1 19.86 ? C1' ADP 301 A 1 
HETATM 18 N N9 ADP . . . B 2 12.091 -2.121 9.869 1 20.32 ? N9 ADP 301 A 1 
HETATM 19 C C8 ADP . . . B 2 11.23 -1.104 10.207 1 19.52 ? C8 ADP 301 A 1 
HETATM 20 N N7 ADP . . . B 2 11.84 -0.056 10.7 1 19.82 ? N7 ADP 301 A 1 
HETATM 21 C C5 ADP . . . B 2 13.176 -0.421 10.726 1 19.81 ? C5 ADP 301 A 1 
HETATM 22 C C6 ADP . . . B 2 14.327 0.254 11.176 1 17.8 ? C6 ADP 301 A 1 
HETATM 23 N N6 ADP . . . B 2 14.305 1.495 11.649 1 18.02 ? N6 ADP 301 A 1 
HETATM 24 N N1 ADP . . . B 2 15.51 -0.407 11.112 1 20.54 ? N1 ADP 301 A 1 
HETATM 25 C C2 ADP . . . B 2 15.518 -1.643 10.597 1 20.39 ? C2 ADP 301 A 1 
HETATM 26 N N3 ADP . . . B 2 14.507 -2.362 10.117 1 20.66 ? N3 ADP 301 A 1 
HETATM 27 C C4 ADP . . . B 2 13.344 -1.699 10.232 1 19.96 ? C4 ADP 301 A 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           38 
_model_server_stats.create_model_time_ms    60 
_model_server_stats.query_time_ms           1132 
_model_server_stats.encode_time_ms          18 
_model_server_stats.element_count           27 
#