data_5LM3
#
_model_server_result.job_id            gyJiuXcc0nKeLiAS11JSOQ 
_model_server_result.datetime_utc      '2024-12-01 07:37:53' 
_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          5lm3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":501}' 
#
_entry.id    5LM3 
#
_exptl.entry_id    5LM3 
_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          113.54 
_cell.angle_gamma         90 
_cell.entry_id            5LM3 
_cell.length_a            55.24 
_cell.length_b            38.92 
_cell.length_c            62.71 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5LM3 
_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               software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_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 
#
_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                     5LM3 
_atom_sites.fract_transf_matrix[1][1]    0.018103 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.007885 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.025694 
_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]    0.017394 
_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 1 501 501 APC APC . 
C 3 EDO A 1 502 506 EDO EDO . 
D 4 HOH A 1 601 601 HOH HOH . 
D 4 HOH A 2 602 602 HOH HOH . 
D 4 HOH A 3 603 609 HOH HOH . 
D 4 HOH A 4 604 608 HOH HOH . 
D 4 HOH A 5 605 606 HOH HOH . 
D 4 HOH A 6 606 604 HOH HOH . 
D 4 HOH A 7 607 613 HOH HOH . 
D 4 HOH A 8 608 611 HOH HOH . 
D 4 HOH A 9 609 616 HOH HOH . 
D 4 HOH A 10 610 619 HOH HOH . 
D 4 HOH A 11 611 637 HOH HOH . 
D 4 HOH A 12 612 615 HOH HOH . 
D 4 HOH A 13 613 614 HOH HOH . 
D 4 HOH A 14 614 622 HOH HOH . 
D 4 HOH A 15 615 618 HOH HOH . 
D 4 HOH A 16 616 635 HOH HOH . 
D 4 HOH A 17 617 638 HOH HOH . 
D 4 HOH A 18 618 617 HOH HOH . 
D 4 HOH A 19 619 620 HOH HOH . 
D 4 HOH A 20 620 621 HOH HOH . 
D 4 HOH A 21 621 610 HOH HOH . 
D 4 HOH A 22 622 632 HOH HOH . 
D 4 HOH A 23 623 629 HOH HOH . 
D 4 HOH A 24 624 626 HOH HOH . 
D 4 HOH A 25 625 612 HOH HOH . 
D 4 HOH A 26 626 625 HOH HOH . 
D 4 HOH A 27 627 623 HOH HOH . 
D 4 HOH A 28 628 627 HOH HOH . 
D 4 HOH A 29 629 631 HOH HOH . 
D 4 HOH A 30 630 624 HOH HOH . 
D 4 HOH A 31 631 605 HOH HOH . 
D 4 HOH A 32 632 633 HOH HOH . 
D 4 HOH A 33 633 636 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 -9.95 -17.757 -8.089 1 61 ? PG APC 501 A 1 
HETATM 2 O O1G APC . . . B 2 -11.219 -18.409 -8.491 1 63.74 ? O1G APC 501 A 1 
HETATM 3 O O2G APC . . . B 2 -9.937 -17.014 -6.801 1 70.99 ? O2G APC 501 A 1 
HETATM 4 O O3G APC . . . B 2 -8.806 -18.901 -7.992 1 72.62 ? O3G APC 501 A 1 
HETATM 5 P PB APC . . . B 2 -8.023 -16.879 -10.066 1 54.23 ? PB APC 501 A 1 
HETATM 6 O O1B APC . . . B 2 -7.952 -15.745 -11.02 1 54.39 ? O1B APC 501 A 1 
HETATM 7 O O2B APC . . . B 2 -6.946 -16.986 -9.055 1 44.44 ? O2B APC 501 A 1 
HETATM 8 O O3B APC . . . B 2 -9.462 -16.768 -9.297 1 65.93 ? O3B APC 501 A 1 
HETATM 9 P PA APC . . . B 2 -7.7 -18.377 -12.679 1 52.48 ? PA APC 501 A 1 
HETATM 10 O O1A APC . . . B 2 -8.689 -17.489 -13.346 1 65.01 ? O1A APC 501 A 1 
HETATM 11 O O2A APC . . . B 2 -7.554 -19.756 -13.204 1 66.2 ? O2A APC 501 A 1 
HETATM 12 C C3A APC . . . B 2 -8.144 -18.446 -10.945 1 45.71 ? C3A APC 501 A 1 
HETATM 13 O O5' APC . . . B 2 -6.253 -17.639 -12.653 1 46.84 ? O5' APC 501 A 1 
HETATM 14 C C5' APC . . . B 2 -5.332 -17.81 -13.749 1 46.16 ? C5' APC 501 A 1 
HETATM 15 C C4' APC . . . B 2 -3.88 -17.441 -13.359 1 51.76 ? C4' APC 501 A 1 
HETATM 16 O O4' APC . . . B 2 -3.81 -16 -13.064 1 50.4 ? O4' APC 501 A 1 
HETATM 17 C C3' APC . . . B 2 -3.454 -18.159 -12.066 1 46.96 ? C3' APC 501 A 1 
HETATM 18 O O3' APC . . . B 2 -2.093 -18.585 -12.169 1 46.08 ? O3' APC 501 A 1 
HETATM 19 C C2' APC . . . B 2 -3.57 -17.115 -10.989 1 43.39 ? C2' APC 501 A 1 
HETATM 20 O O2' APC . . . B 2 -2.58 -17.358 -9.983 1 47.55 ? O2' APC 501 A 1 
HETATM 21 C C1' APC . . . B 2 -3.251 -15.826 -11.722 1 43.99 ? C1' APC 501 A 1 
HETATM 22 N N9 APC . . . B 2 -3.813 -14.637 -11.029 1 43 ? N9 APC 501 A 1 
HETATM 23 C C8 APC . . . B 2 -5.108 -14.289 -10.992 1 51.24 ? C8 APC 501 A 1 
HETATM 24 N N7 APC . . . B 2 -5.246 -13.168 -10.272 1 59.63 ? N7 APC 501 A 1 
HETATM 25 C C5 APC . . . B 2 -4.046 -12.8 -9.849 1 54.05 ? C5 APC 501 A 1 
HETATM 26 C C6 APC . . . B 2 -3.596 -11.732 -9.075 1 52.49 ? C6 APC 501 A 1 
HETATM 27 N N6 APC . . . B 2 -4.461 -10.83 -8.607 1 43.9 ? N6 APC 501 A 1 
HETATM 28 N N1 APC . . . B 2 -2.271 -11.621 -8.803 1 58.6 ? N1 APC 501 A 1 
HETATM 29 C C2 APC . . . B 2 -1.351 -12.584 -9.3 1 51.25 ? C2 APC 501 A 1 
HETATM 30 N N3 APC . . . B 2 -1.796 -13.604 -10.04 1 49.52 ? N3 APC 501 A 1 
HETATM 31 C C4 APC . . . B 2 -3.123 -13.735 -10.327 1 50.8 ? C4 APC 501 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           370 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           31 
#