data_4M5J
#
_model_server_result.job_id            B2Q5CbL5MOa0EXGXiDuEcA 
_model_server_result.datetime_utc      '2024-11-26 10:18:36' 
_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          4m5j 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":301}' 
#
_entry.id    4M5J 
#
_exptl.entry_id    4M5J 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              505.208 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' 
_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          113.76 
_cell.angle_gamma         90 
_cell.entry_id            4M5J 
_cell.length_a            36.458 
_cell.length_b            58.264 
_cell.length_c            38.374 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4M5J 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
#
_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                      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 OD2 ASP 99 A ASP 95 1_555 D MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? 
metalc ? metalc2 A OD1 ASP 99 A ASP 95 1_555 E MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? 
metalc ? metalc3 A OD2 ASP 101 A ASP 97 1_555 D MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? 
metalc ? metalc4 A OD1 ASP 101 A ASP 97 1_555 E MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? 
metalc ? metalc5 B O1B APC . A APC 301 1_555 D MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? 
metalc ? metalc6 B O2G APC . A APC 301 1_555 D MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.487 ? 
metalc ? metalc7 B O1B APC . A APC 301 1_555 E MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? 
metalc ? metalc8 B O1A APC . A APC 301 1_555 E MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? 
metalc ? metalc9 E MG MG . A MG 304 1_555 H O HOH . A HOH 459 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
metalc ? metalc10 E MG MG . A MG 304 1_555 H O HOH . A HOH 460 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? 
#
_chem_comp.formula           'C11 H18 N5 O12 P3' 
_chem_comp.formula_weight    505.208 
_chem_comp.id                APC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE" 
#
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
PG O1G APC doub 13 n n 
PG O2G APC sing 14 n n 
PG O3G APC sing 15 n n 
PG O3B APC sing 16 n n 
O2G HOG2 APC sing 17 n n 
O3G HOG3 APC sing 18 n n 
PB O1B APC doub 19 n n 
PB O2B APC sing 20 n n 
PB O3B APC sing 21 n n 
PB C3A APC sing 22 n n 
O2B HOB2 APC sing 23 n n 
PA O1A APC doub 24 n n 
PA O2A APC sing 25 n n 
PA C3A APC sing 26 n n 
PA O5' APC sing 27 n n 
O2A HOA2 APC sing 28 n n 
C3A H3A1 APC sing 29 n n 
C3A H3A2 APC sing 30 n n 
O5' C5' APC sing 31 n n 
C5' C4' APC sing 32 n n 
C5' "H5'1" APC sing 33 n n 
C5' "H5'2" APC sing 34 n n 
C4' O4' APC sing 35 n n 
C4' C3' APC sing 36 n n 
C4' H4' APC sing 37 n n 
O4' C1' APC sing 38 n n 
C3' O3' APC sing 39 n n 
C3' C2' APC sing 40 n n 
C3' H3' APC sing 41 n n 
O3' HO3' APC sing 42 n n 
C2' O2' APC sing 43 n n 
C2' C1' APC sing 44 n n 
C2' H2' APC sing 45 n n 
O2' HO2' APC sing 46 n n 
C1' N9 APC sing 47 n n 
C1' H1' APC sing 48 n n 
N9 C8 APC sing 49 n y 
N9 C4 APC sing 50 n y 
C8 N7 APC doub 51 n y 
C8 H8 APC sing 52 n n 
N7 C5 APC sing 53 n y 
C5 C6 APC sing 54 n y 
C5 C4 APC doub 55 n y 
C6 N6 APC sing 56 n n 
C6 N1 APC doub 57 n y 
N6 HN61 APC sing 58 n n 
N6 HN62 APC sing 59 n n 
N1 C2 APC sing 60 n y 
C2 N3 APC doub 61 n y 
C2 H2 APC sing 62 n n 
N3 C4 APC sing 63 n y 
#
_atom_sites.entry_id                     4M5J 
_atom_sites.fract_transf_matrix[1][1]    0.027429 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.012074 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.017163 
_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]    0.028472 
_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 APC A 1 301 301 APC APC . 
C 3 YH5 A 1 302 401 YH5 YH5 . 
D 4 MG A 1 303 201 MG MG . 
E 4 MG A 1 304 202 MG MG . 
F 5 CL A 1 305 501 CL CL . 
G 5 CL A 1 306 502 CL CL . 
H 6 HOH A 1 401 1 HOH HOH . 
H 6 HOH A 2 402 2 HOH HOH . 
H 6 HOH A 3 403 3 HOH HOH . 
H 6 HOH A 4 404 4 HOH HOH . 
H 6 HOH A 5 405 5 HOH HOH . 
H 6 HOH A 6 406 6 HOH HOH . 
H 6 HOH A 7 407 7 HOH HOH . 
H 6 HOH A 8 408 8 HOH HOH . 
H 6 HOH A 9 409 9 HOH HOH . 
H 6 HOH A 10 410 10 HOH HOH . 
H 6 HOH A 11 411 11 HOH HOH . 
H 6 HOH A 12 412 12 HOH HOH . 
H 6 HOH A 13 413 13 HOH HOH . 
H 6 HOH A 14 414 14 HOH HOH . 
H 6 HOH A 15 415 15 HOH HOH . 
H 6 HOH A 16 416 16 HOH HOH . 
H 6 HOH A 17 417 17 HOH HOH . 
H 6 HOH A 18 418 18 HOH HOH . 
H 6 HOH A 19 419 19 HOH HOH . 
H 6 HOH A 20 420 20 HOH HOH . 
H 6 HOH A 21 421 21 HOH HOH . 
H 6 HOH A 22 422 22 HOH HOH . 
H 6 HOH A 23 423 23 HOH HOH . 
H 6 HOH A 24 424 24 HOH HOH . 
H 6 HOH A 25 425 25 HOH HOH . 
H 6 HOH A 26 426 26 HOH HOH . 
H 6 HOH A 27 427 27 HOH HOH . 
H 6 HOH A 28 428 28 HOH HOH . 
H 6 HOH A 29 429 29 HOH HOH . 
H 6 HOH A 30 430 30 HOH HOH . 
H 6 HOH A 31 431 31 HOH HOH . 
H 6 HOH A 32 432 32 HOH HOH . 
H 6 HOH A 33 433 33 HOH HOH . 
H 6 HOH A 34 434 34 HOH HOH . 
H 6 HOH A 35 435 35 HOH HOH . 
H 6 HOH A 36 436 36 HOH HOH . 
H 6 HOH A 37 437 37 HOH HOH . 
H 6 HOH A 38 438 38 HOH HOH . 
H 6 HOH A 39 439 39 HOH HOH . 
H 6 HOH A 40 440 40 HOH HOH . 
H 6 HOH A 41 441 41 HOH HOH . 
H 6 HOH A 42 442 42 HOH HOH . 
H 6 HOH A 43 443 43 HOH HOH . 
H 6 HOH A 44 444 44 HOH HOH . 
H 6 HOH A 45 445 45 HOH HOH . 
H 6 HOH A 46 446 46 HOH HOH . 
H 6 HOH A 47 447 47 HOH HOH . 
H 6 HOH A 48 448 48 HOH HOH . 
H 6 HOH A 49 449 49 HOH HOH . 
H 6 HOH A 50 450 50 HOH HOH . 
H 6 HOH A 51 451 51 HOH HOH . 
H 6 HOH A 52 452 52 HOH HOH . 
H 6 HOH A 53 453 53 HOH HOH . 
H 6 HOH A 54 454 54 HOH HOH . 
H 6 HOH A 55 455 55 HOH HOH . 
H 6 HOH A 56 456 56 HOH HOH . 
H 6 HOH A 57 457 57 HOH HOH . 
H 6 HOH A 58 458 58 HOH HOH . 
H 6 HOH A 59 459 59 HOH HOH . 
H 6 HOH A 60 460 60 HOH HOH . 
H 6 HOH A 61 461 61 HOH HOH . 
H 6 HOH A 62 462 62 HOH HOH . 
H 6 HOH A 63 463 63 HOH HOH . 
H 6 HOH A 64 464 64 HOH HOH . 
H 6 HOH A 65 465 65 HOH HOH . 
H 6 HOH A 66 466 66 HOH HOH . 
H 6 HOH A 67 467 67 HOH HOH . 
H 6 HOH A 68 468 68 HOH HOH . 
H 6 HOH A 69 469 69 HOH HOH . 
H 6 HOH A 70 470 70 HOH HOH . 
H 6 HOH A 71 471 71 HOH HOH . 
H 6 HOH A 72 472 72 HOH HOH . 
H 6 HOH A 73 473 73 HOH HOH . 
H 6 HOH A 74 474 74 HOH HOH . 
H 6 HOH A 75 475 75 HOH HOH . 
H 6 HOH A 76 476 76 HOH HOH . 
H 6 HOH A 77 477 77 HOH HOH . 
H 6 HOH A 78 478 78 HOH HOH . 
H 6 HOH A 79 479 79 HOH HOH . 
H 6 HOH A 80 480 80 HOH HOH . 
H 6 HOH A 81 481 81 HOH HOH . 
H 6 HOH A 82 482 82 HOH HOH . 
H 6 HOH A 83 483 83 HOH HOH . 
H 6 HOH A 84 484 84 HOH HOH . 
H 6 HOH A 85 485 85 HOH HOH . 
H 6 HOH A 86 486 86 HOH HOH . 
H 6 HOH A 87 487 87 HOH HOH . 
H 6 HOH A 88 488 88 HOH HOH . 
H 6 HOH A 89 489 89 HOH HOH . 
H 6 HOH A 90 490 90 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 PG APC . . . B 2 60.657 15.536 38.969 1 36.91 ? PG APC 301 A 1 
HETATM 2 O O1G APC . . . B 2 59.936 16.87 38.787 1 39.67 ? O1G APC 301 A 1 
HETATM 3 O O2G APC . . . B 2 59.854 14.261 38.763 1 35.37 ? O2G APC 301 A 1 
HETATM 4 O O3G APC . . . B 2 61.564 15.475 40.176 1 49.33 ? O3G APC 301 A 1 
HETATM 5 P PB APC . . . B 2 62.822 14.532 37.492 1 47.61 ? PB APC 301 A 1 
HETATM 6 O O1B APC . . . B 2 62.302 13.191 37.876 1 54.84 ? O1B APC 301 A 1 
HETATM 7 O O2B APC . . . B 2 63.212 14.562 35.946 1 45.68 ? O2B APC 301 A 1 
HETATM 8 O O3B APC . . . B 2 61.654 15.611 37.717 1 31.59 ? O3B APC 301 A 1 
HETATM 9 P PA APC . . . B 2 65.469 13.893 39.053 1 44.75 ? PA APC 301 A 1 
HETATM 10 O O1A APC . . . B 2 65.162 12.46 38.729 1 38.19 ? O1A APC 301 A 1 
HETATM 11 O O2A APC . . . B 2 66.762 14.407 38.242 1 50.26 ? O2A APC 301 A 1 
HETATM 12 C C3A APC . . . B 2 64.171 15.074 38.578 1 66.77 ? C3A APC 301 A 1 
HETATM 13 O O5' APC . . . B 2 65.722 14.062 40.645 1 33.79 ? O5' APC 301 A 1 
HETATM 14 C C5' APC . . . B 2 66.995 14.393 41.203 1 41.54 ? C5' APC 301 A 1 
HETATM 15 C C4' APC . . . B 2 66.943 14.552 42.735 1 46.09 ? C4' APC 301 A 1 
HETATM 16 O O4' APC . . . B 2 65.614 14.585 43.312 1 40.83 ? O4' APC 301 A 1 
HETATM 17 C C3' APC . . . B 2 67.663 13.417 43.458 1 43.89 ? C3' APC 301 A 1 
HETATM 18 O O3' APC . . . B 2 69.004 13.804 43.755 1 52.36 ? O3' APC 301 A 1 
HETATM 19 C C2' APC . . . B 2 66.887 13.189 44.747 1 35.03 ? C2' APC 301 A 1 
HETATM 20 O O2' APC . . . B 2 67.735 13.46 45.88 1 45.28 ? O2' APC 301 A 1 
HETATM 21 C C1' APC . . . B 2 65.746 14.206 44.694 1 31.67 ? C1' APC 301 A 1 
HETATM 22 N N9 APC . . . B 2 64.443 13.729 45.246 1 28.4 ? N9 APC 301 A 1 
HETATM 23 C C8 APC . . . B 2 63.685 14.412 46.13 1 31.92 ? C8 APC 301 A 1 
HETATM 24 N N7 APC . . . B 2 62.553 13.735 46.444 1 28.38 ? N7 APC 301 A 1 
HETATM 25 C C5 APC . . . B 2 62.557 12.597 45.721 1 25.52 ? C5 APC 301 A 1 
HETATM 26 C C6 APC . . . B 2 61.66 11.43 45.589 1 23.21 ? C6 APC 301 A 1 
HETATM 27 N N6 APC . . . B 2 60.498 11.404 46.288 1 21.83 ? N6 APC 301 A 1 
HETATM 28 N N1 APC . . . B 2 62.029 10.444 44.735 1 22.75 ? N1 APC 301 A 1 
HETATM 29 C C2 APC . . . B 2 63.184 10.498 44.05 1 24.32 ? C2 APC 301 A 1 
HETATM 30 N N3 APC . . . B 2 64.041 11.527 44.131 1 25.68 ? N3 APC 301 A 1 
HETATM 31 C C4 APC . . . B 2 63.806 12.582 44.946 1 25.62 ? C4 APC 301 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           343 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           31 
#