data_4YXJ
#
_model_server_result.job_id            wmgGgJIizKWaDhXbkxlfLQ 
_model_server_result.datetime_utc      '2024-10-19 11:32:52' 
_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          4yxj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":401}' 
#
_entry.id    4YXJ 
#
_exptl.entry_id    4YXJ 
_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    2 
_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            4YXJ 
_cell.length_a            108.25 
_cell.length_b            108.25 
_cell.length_c            166.4 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4YXJ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        90 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 4 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4 
#
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_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 0 -108.25 0 
3 'crystal symmetry operation' 3_445 -y-1/2,x-1/2,z 0 -1 0 1 0 0 0 0 1 -54.125 -54.125 0 
4 'crystal symmetry operation' 4_545 y+1/2,-x-1/2,z 0 1 0 -1 0 0 0 0 1 54.125 -54.125 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 D N N 
#
_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                     4YXJ 
_atom_sites.fract_transf_matrix[1][1]    0.009238 
_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]    0.009238 
_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]    0.00601 
_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 2 APC A 1 401 1 APC APC . 
D 2 APC B 1 401 2 APC APC . 
E 3 HOH A 1 501 7 HOH HOH . 
E 3 HOH A 2 502 119 HOH HOH . 
E 3 HOH A 3 503 60 HOH HOH . 
E 3 HOH A 4 504 168 HOH HOH . 
E 3 HOH A 5 505 108 HOH HOH . 
E 3 HOH A 6 506 132 HOH HOH . 
E 3 HOH A 7 507 81 HOH HOH . 
E 3 HOH A 8 508 69 HOH HOH . 
E 3 HOH A 9 509 89 HOH HOH . 
E 3 HOH A 10 510 42 HOH HOH . 
E 3 HOH A 11 511 50 HOH HOH . 
E 3 HOH A 12 512 11 HOH HOH . 
E 3 HOH A 13 513 88 HOH HOH . 
E 3 HOH A 14 514 123 HOH HOH . 
E 3 HOH A 15 515 169 HOH HOH . 
E 3 HOH A 16 516 100 HOH HOH . 
E 3 HOH A 17 517 104 HOH HOH . 
E 3 HOH A 18 518 2 HOH HOH . 
E 3 HOH A 19 519 56 HOH HOH . 
E 3 HOH A 20 520 174 HOH HOH . 
E 3 HOH A 21 521 94 HOH HOH . 
E 3 HOH A 22 522 92 HOH HOH . 
E 3 HOH A 23 523 8 HOH HOH . 
E 3 HOH A 24 524 9 HOH HOH . 
E 3 HOH A 25 525 13 HOH HOH . 
E 3 HOH A 26 526 131 HOH HOH . 
E 3 HOH A 27 527 120 HOH HOH . 
E 3 HOH A 28 528 45 HOH HOH . 
E 3 HOH A 29 529 117 HOH HOH . 
E 3 HOH A 30 530 16 HOH HOH . 
E 3 HOH A 31 531 124 HOH HOH . 
E 3 HOH A 32 532 48 HOH HOH . 
E 3 HOH A 33 533 24 HOH HOH . 
E 3 HOH A 34 534 70 HOH HOH . 
E 3 HOH A 35 535 114 HOH HOH . 
E 3 HOH A 36 536 86 HOH HOH . 
E 3 HOH A 37 537 38 HOH HOH . 
E 3 HOH A 38 538 125 HOH HOH . 
E 3 HOH A 39 539 166 HOH HOH . 
E 3 HOH A 40 540 103 HOH HOH . 
E 3 HOH A 41 541 40 HOH HOH . 
E 3 HOH A 42 542 73 HOH HOH . 
E 3 HOH A 43 543 5 HOH HOH . 
E 3 HOH A 44 544 170 HOH HOH . 
E 3 HOH A 45 545 18 HOH HOH . 
E 3 HOH A 46 546 26 HOH HOH . 
E 3 HOH A 47 547 15 HOH HOH . 
E 3 HOH A 48 548 3 HOH HOH . 
E 3 HOH A 49 549 95 HOH HOH . 
E 3 HOH A 50 550 146 HOH HOH . 
E 3 HOH A 51 551 19 HOH HOH . 
E 3 HOH A 52 552 62 HOH HOH . 
E 3 HOH A 53 553 67 HOH HOH . 
E 3 HOH A 54 554 135 HOH HOH . 
E 3 HOH A 55 555 51 HOH HOH . 
E 3 HOH A 56 556 85 HOH HOH . 
E 3 HOH A 57 557 66 HOH HOH . 
E 3 HOH A 58 558 140 HOH HOH . 
E 3 HOH A 59 559 98 HOH HOH . 
E 3 HOH A 60 560 113 HOH HOH . 
E 3 HOH A 61 561 165 HOH HOH . 
E 3 HOH A 62 562 71 HOH HOH . 
E 3 HOH A 63 563 105 HOH HOH . 
E 3 HOH A 64 564 39 HOH HOH . 
E 3 HOH A 65 565 54 HOH HOH . 
E 3 HOH A 66 566 107 HOH HOH . 
E 3 HOH A 67 567 59 HOH HOH . 
E 3 HOH A 68 568 176 HOH HOH . 
E 3 HOH A 69 569 171 HOH HOH . 
E 3 HOH A 70 570 115 HOH HOH . 
E 3 HOH A 71 571 97 HOH HOH . 
E 3 HOH A 72 572 52 HOH HOH . 
E 3 HOH A 73 573 82 HOH HOH . 
E 3 HOH A 74 574 65 HOH HOH . 
E 3 HOH A 75 575 33 HOH HOH . 
E 3 HOH A 76 576 121 HOH HOH . 
E 3 HOH A 77 577 77 HOH HOH . 
E 3 HOH A 78 578 139 HOH HOH . 
E 3 HOH A 79 579 112 HOH HOH . 
E 3 HOH A 80 580 137 HOH HOH . 
E 3 HOH A 81 581 41 HOH HOH . 
E 3 HOH A 82 582 145 HOH HOH . 
E 3 HOH A 83 583 75 HOH HOH . 
E 3 HOH A 84 584 173 HOH HOH . 
E 3 HOH A 85 585 134 HOH HOH . 
E 3 HOH A 86 586 141 HOH HOH . 
E 3 HOH A 87 587 133 HOH HOH . 
E 3 HOH A 88 588 143 HOH HOH . 
E 3 HOH A 89 589 72 HOH HOH . 
E 3 HOH A 90 590 178 HOH HOH . 
E 3 HOH A 91 591 136 HOH HOH . 
E 3 HOH A 92 592 172 HOH HOH . 
E 3 HOH A 93 593 150 HOH HOH . 
E 3 HOH A 94 594 142 HOH HOH . 
E 3 HOH A 95 595 116 HOH HOH . 
E 3 HOH A 96 596 144 HOH HOH . 
E 3 HOH A 97 597 167 HOH HOH . 
E 3 HOH A 98 598 128 HOH HOH . 
E 3 HOH A 99 599 177 HOH HOH . 
E 3 HOH A 100 600 187 HOH HOH . 
E 3 HOH A 101 601 99 HOH HOH . 
E 3 HOH A 102 602 175 HOH HOH . 
E 3 HOH A 103 603 31 HOH HOH . 
E 3 HOH A 104 604 83 HOH HOH . 
E 3 HOH A 105 605 126 HOH HOH . 
E 3 HOH A 106 606 46 HOH HOH . 
F 3 HOH B 1 501 161 HOH HOH . 
F 3 HOH B 2 502 14 HOH HOH . 
F 3 HOH B 3 503 109 HOH HOH . 
F 3 HOH B 4 504 55 HOH HOH . 
F 3 HOH B 5 505 111 HOH HOH . 
F 3 HOH B 6 506 25 HOH HOH . 
F 3 HOH B 7 507 61 HOH HOH . 
F 3 HOH B 8 508 21 HOH HOH . 
F 3 HOH B 9 509 17 HOH HOH . 
F 3 HOH B 10 510 162 HOH HOH . 
F 3 HOH B 11 511 44 HOH HOH . 
F 3 HOH B 12 512 35 HOH HOH . 
F 3 HOH B 13 513 78 HOH HOH . 
F 3 HOH B 14 514 76 HOH HOH . 
F 3 HOH B 15 515 63 HOH HOH . 
F 3 HOH B 16 516 101 HOH HOH . 
F 3 HOH B 17 517 159 HOH HOH . 
F 3 HOH B 18 518 27 HOH HOH . 
F 3 HOH B 19 519 20 HOH HOH . 
F 3 HOH B 20 520 79 HOH HOH . 
F 3 HOH B 21 521 64 HOH HOH . 
F 3 HOH B 22 522 1 HOH HOH . 
F 3 HOH B 23 523 118 HOH HOH . 
F 3 HOH B 24 524 152 HOH HOH . 
F 3 HOH B 25 525 28 HOH HOH . 
F 3 HOH B 26 526 30 HOH HOH . 
F 3 HOH B 27 527 23 HOH HOH . 
F 3 HOH B 28 528 12 HOH HOH . 
F 3 HOH B 29 529 29 HOH HOH . 
F 3 HOH B 30 530 36 HOH HOH . 
F 3 HOH B 31 531 102 HOH HOH . 
F 3 HOH B 32 532 37 HOH HOH . 
F 3 HOH B 33 533 43 HOH HOH . 
F 3 HOH B 34 534 127 HOH HOH . 
F 3 HOH B 35 535 22 HOH HOH . 
F 3 HOH B 36 536 154 HOH HOH . 
F 3 HOH B 37 537 110 HOH HOH . 
F 3 HOH B 38 538 148 HOH HOH . 
F 3 HOH B 39 539 68 HOH HOH . 
F 3 HOH B 40 540 49 HOH HOH . 
F 3 HOH B 41 541 74 HOH HOH . 
F 3 HOH B 42 542 6 HOH HOH . 
F 3 HOH B 43 543 4 HOH HOH . 
F 3 HOH B 44 544 122 HOH HOH . 
F 3 HOH B 45 545 10 HOH HOH . 
F 3 HOH B 46 546 151 HOH HOH . 
F 3 HOH B 47 547 53 HOH HOH . 
F 3 HOH B 48 548 156 HOH HOH . 
F 3 HOH B 49 549 58 HOH HOH . 
F 3 HOH B 50 550 32 HOH HOH . 
F 3 HOH B 51 551 155 HOH HOH . 
F 3 HOH B 52 552 90 HOH HOH . 
F 3 HOH B 53 553 91 HOH HOH . 
F 3 HOH B 54 554 34 HOH HOH . 
F 3 HOH B 55 555 106 HOH HOH . 
F 3 HOH B 56 556 138 HOH HOH . 
F 3 HOH B 57 557 186 HOH HOH . 
F 3 HOH B 58 558 160 HOH HOH . 
F 3 HOH B 59 559 164 HOH HOH . 
F 3 HOH B 60 560 147 HOH HOH . 
F 3 HOH B 61 561 129 HOH HOH . 
F 3 HOH B 62 562 80 HOH HOH . 
F 3 HOH B 63 563 163 HOH HOH . 
F 3 HOH B 64 564 153 HOH HOH . 
F 3 HOH B 65 565 157 HOH HOH . 
F 3 HOH B 66 566 182 HOH HOH . 
F 3 HOH B 67 567 84 HOH HOH . 
F 3 HOH B 68 568 180 HOH HOH . 
F 3 HOH B 69 569 185 HOH HOH . 
F 3 HOH B 70 570 149 HOH HOH . 
F 3 HOH B 71 571 184 HOH HOH . 
F 3 HOH B 72 572 179 HOH HOH . 
F 3 HOH B 73 573 47 HOH HOH . 
F 3 HOH B 74 574 93 HOH HOH . 
F 3 HOH B 75 575 158 HOH HOH . 
F 3 HOH B 76 576 181 HOH HOH . 
F 3 HOH B 77 577 87 HOH HOH . 
F 3 HOH B 78 578 183 HOH HOH . 
F 3 HOH B 79 579 96 HOH HOH . 
F 3 HOH B 80 580 57 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 . . . D 2 6.691 -39.731 -46.331 1 98.61 ? PG APC 401 B 1 
HETATM 2 O O1G APC . . . D 2 6.237 -40.201 -47.694 1 78.69 ? O1G APC 401 B 1 
HETATM 3 O O2G APC . . . D 2 6.091 -38.36 -46.037 1 78.18 ? O2G APC 401 B 1 
HETATM 4 O O3G APC . . . D 2 6.296 -40.757 -45.277 1 84.25 ? O3G APC 401 B 1 
HETATM 5 P PB APC . . . D 2 9.197 -40.266 -45.317 1 70.99 ? PB APC 401 B 1 
HETATM 6 O O1B APC . . . D 2 9.557 -41.674 -45.75 1 60.35 ? O1B APC 401 B 1 
HETATM 7 O O2B APC . . . D 2 8.621 -40.347 -43.929 1 67.82 ? O2B APC 401 B 1 
HETATM 8 O O3B APC . . . D 2 8.226 -39.614 -46.319 1 81.75 ? O3B APC 401 B 1 
HETATM 9 P PA APC . . . D 2 10.722 -37.889 -44.085 1 62.52 ? PA APC 401 B 1 
HETATM 10 O O1A APC . . . D 2 10.653 -36.526 -44.727 1 48.29 ? O1A APC 401 B 1 
HETATM 11 O O2A APC . . . D 2 9.629 -37.959 -43.03 1 70.52 ? O2A APC 401 B 1 
HETATM 12 C C3A APC . . . D 2 10.644 -39.175 -45.406 1 54.68 ? C3A APC 401 B 1 
HETATM 13 O O5' APC . . . D 2 12.151 -38.101 -43.362 1 53.2 ? O5' APC 401 B 1 
HETATM 14 C C5' APC . . . D 2 12.223 -38.792 -42.094 1 51.81 ? C5' APC 401 B 1 
HETATM 15 C C4' APC . . . D 2 13.492 -39.699 -42.029 1 47.52 ? C4' APC 401 B 1 
HETATM 16 O O4' APC . . . D 2 14.374 -39.428 -42.963 1 47.24 ? O4' APC 401 B 1 
HETATM 17 C C3' APC . . . D 2 14.212 -39.414 -40.731 1 43.69 ? C3' APC 401 B 1 
HETATM 18 O O3' APC . . . D 2 13.688 -40.168 -39.736 1 57.66 ? O3' APC 401 B 1 
HETATM 19 C C2' APC . . . D 2 15.685 -39.78 -41.046 1 43.88 ? C2' APC 401 B 1 
HETATM 20 O O2' APC . . . D 2 15.981 -41.207 -40.688 1 43.84 ? O2' APC 401 B 1 
HETATM 21 C C1' APC . . . D 2 15.852 -39.503 -42.31 1 40.94 ? C1' APC 401 B 1 
HETATM 22 N N9 APC . . . D 2 16.389 -38.185 -42.274 1 36.34 ? N9 APC 401 B 1 
HETATM 23 C C8 APC . . . D 2 15.684 -37.023 -42.341 1 37.63 ? C8 APC 401 B 1 
HETATM 24 N N7 APC . . . D 2 16.555 -35.996 -42.209 1 36.43 ? N7 APC 401 B 1 
HETATM 25 C C5 APC . . . D 2 17.803 -36.519 -42.047 1 35.86 ? C5 APC 401 B 1 
HETATM 26 C C6 APC . . . D 2 19.027 -35.89 -41.883 1 34.26 ? C6 APC 401 B 1 
HETATM 27 N N6 APC . . . D 2 19.455 -34.522 -41.812 1 32.04 ? N6 APC 401 B 1 
HETATM 28 N N1 APC . . . D 2 20.15 -36.621 -41.739 1 29.34 ? N1 APC 401 B 1 
HETATM 29 C C2 APC . . . D 2 20.058 -37.991 -41.768 1 33.94 ? C2 APC 401 B 1 
HETATM 30 N N3 APC . . . D 2 18.839 -38.615 -41.933 1 34.97 ? N3 APC 401 B 1 
HETATM 31 C C4 APC . . . D 2 17.706 -37.87 -42.068 1 33.05 ? C4 APC 401 B 1 
#
_model_server_stats.io_time_ms              43 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           328 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           31 
#