data_6JDL
#
_model_server_result.job_id            JJPdFTZPDO3Uq5MFL8VQZA 
_model_server_result.datetime_utc      '2024-11-25 09:05:23' 
_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          6jdl 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":401}' 
#
_entry.id    6JDL 
#
_exptl.entry_id    6JDL 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              523.247 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE 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          90 
_cell.angle_gamma         120 
_cell.entry_id            6JDL 
_cell.length_a            105.011 
_cell.length_b            105.011 
_cell.length_c            43.191 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6JDL 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        170 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65' 
#
_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 
_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 OE1 GLU 45 A GLU 181 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.647 ? 
metalc ? metalc2 B O2G AGS . A AGS 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? 
metalc ? metalc3 C MG MG . A MG 402 1_555 D O HOH . A HOH 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? 
metalc ? metalc4 C MG MG . A MG 402 1_555 D O HOH . A HOH 534 6_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.53 ? 
#
_chem_comp.formula           'C10 H16 N5 O12 P3 S' 
_chem_comp.formula_weight    523.247 
_chem_comp.id                AGS 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "ATP-GAMMA-S;ADENOSINE 5'-(3-THIOTRIPHOSPHATE);ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE" 
#
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 S1G AGS doub 1 n n 
PG O2G AGS sing 2 n n 
PG O3G AGS sing 3 n n 
PG O3B AGS sing 4 n n 
PB O1B AGS doub 5 n n 
PB O2B AGS sing 6 n n 
PB O3B AGS sing 7 n n 
PB O3A AGS sing 8 n n 
PA O1A AGS doub 9 n n 
PA O2A AGS sing 10 n n 
PA O3A AGS sing 11 n n 
PA O5' AGS sing 12 n n 
O5' C5' AGS sing 13 n n 
C5' C4' AGS sing 14 n n 
C4' O4' AGS sing 15 n n 
C4' C3' AGS sing 16 n n 
O4' C1' AGS sing 17 n n 
C3' O3' AGS sing 18 n n 
C3' C2' AGS sing 19 n n 
C2' O2' AGS sing 20 n n 
C2' C1' AGS sing 21 n n 
C1' N9 AGS sing 22 n n 
N9 C8 AGS sing 23 n y 
N9 C4 AGS sing 24 n y 
C8 N7 AGS doub 25 n y 
N7 C5 AGS sing 26 n y 
C5 C6 AGS sing 27 n y 
C5 C4 AGS doub 28 n y 
C6 N6 AGS sing 29 n n 
C6 N1 AGS doub 30 n y 
N1 C2 AGS sing 31 n y 
C2 N3 AGS doub 32 n y 
N3 C4 AGS sing 33 n y 
O2G HOG2 AGS sing 34 n n 
O3G H21 AGS sing 35 n n 
O2B HOB2 AGS sing 36 n n 
O2A HOA2 AGS sing 37 n n 
C5' "H5'1" AGS sing 38 n n 
C5' "H5'2" AGS sing 39 n n 
C4' H4' AGS sing 40 n n 
C3' H3' AGS sing 41 n n 
O3' HO3' AGS sing 42 n n 
C2' H2' AGS sing 43 n n 
O2' HO2' AGS sing 44 n n 
C1' H1' AGS sing 45 n n 
C8 H8 AGS sing 46 n n 
N6 HN61 AGS sing 47 n n 
N6 HN62 AGS sing 48 n n 
C2 H2 AGS sing 49 n n 
#
_atom_sites.entry_id                     6JDL 
_atom_sites.fract_transf_matrix[1][1]    0.009523 
_atom_sites.fract_transf_matrix[1][2]    0.005498 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010996 
_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]    0.023153 
_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 AGS A 1 401 401 AGS AGS . 
C 3 MG A 1 402 1 MG MG . 
D 4 HOH A 1 501 52 HOH HOH . 
D 4 HOH A 2 502 9 HOH HOH . 
D 4 HOH A 3 503 60 HOH HOH . 
D 4 HOH A 4 504 44 HOH HOH . 
D 4 HOH A 5 505 16 HOH HOH . 
D 4 HOH A 6 506 45 HOH HOH . 
D 4 HOH A 7 507 35 HOH HOH . 
D 4 HOH A 8 508 51 HOH HOH . 
D 4 HOH A 9 509 23 HOH HOH . 
D 4 HOH A 10 510 12 HOH HOH . 
D 4 HOH A 11 511 41 HOH HOH . 
D 4 HOH A 12 512 13 HOH HOH . 
D 4 HOH A 13 513 71 HOH HOH . 
D 4 HOH A 14 514 14 HOH HOH . 
D 4 HOH A 15 515 7 HOH HOH . 
D 4 HOH A 16 516 56 HOH HOH . 
D 4 HOH A 17 517 57 HOH HOH . 
D 4 HOH A 18 518 1 HOH HOH . 
D 4 HOH A 19 519 28 HOH HOH . 
D 4 HOH A 20 520 5 HOH HOH . 
D 4 HOH A 21 521 58 HOH HOH . 
D 4 HOH A 22 522 8 HOH HOH . 
D 4 HOH A 23 523 46 HOH HOH . 
D 4 HOH A 24 524 3 HOH HOH . 
D 4 HOH A 25 525 21 HOH HOH . 
D 4 HOH A 26 526 48 HOH HOH . 
D 4 HOH A 27 527 19 HOH HOH . 
D 4 HOH A 28 528 26 HOH HOH . 
D 4 HOH A 29 529 34 HOH HOH . 
D 4 HOH A 30 530 2 HOH HOH . 
D 4 HOH A 31 531 6 HOH HOH . 
D 4 HOH A 32 532 49 HOH HOH . 
D 4 HOH A 33 533 73 HOH HOH . 
D 4 HOH A 34 534 11 HOH HOH . 
D 4 HOH A 35 535 15 HOH HOH . 
D 4 HOH A 36 536 32 HOH HOH . 
D 4 HOH A 37 537 25 HOH HOH . 
D 4 HOH A 38 538 20 HOH HOH . 
D 4 HOH A 39 539 47 HOH HOH . 
D 4 HOH A 40 540 65 HOH HOH . 
D 4 HOH A 41 541 72 HOH HOH . 
D 4 HOH A 42 542 17 HOH HOH . 
D 4 HOH A 43 543 59 HOH HOH . 
D 4 HOH A 44 544 42 HOH HOH . 
D 4 HOH A 45 545 30 HOH HOH . 
D 4 HOH A 46 546 50 HOH HOH . 
D 4 HOH A 47 547 10 HOH HOH . 
D 4 HOH A 48 548 37 HOH HOH . 
D 4 HOH A 49 549 22 HOH HOH . 
D 4 HOH A 50 550 31 HOH HOH . 
D 4 HOH A 51 551 74 HOH HOH . 
D 4 HOH A 52 552 70 HOH HOH . 
D 4 HOH A 53 553 40 HOH HOH . 
D 4 HOH A 54 554 18 HOH HOH . 
D 4 HOH A 55 555 33 HOH HOH . 
D 4 HOH A 56 556 27 HOH HOH . 
D 4 HOH A 57 557 4 HOH HOH . 
D 4 HOH A 58 558 54 HOH HOH . 
D 4 HOH A 59 559 24 HOH HOH . 
D 4 HOH A 60 560 61 HOH HOH . 
D 4 HOH A 61 561 53 HOH HOH . 
D 4 HOH A 62 562 64 HOH HOH . 
D 4 HOH A 63 563 29 HOH HOH . 
D 4 HOH A 64 564 68 HOH HOH . 
D 4 HOH A 65 565 43 HOH HOH . 
D 4 HOH A 66 566 36 HOH HOH . 
D 4 HOH A 67 567 66 HOH HOH . 
D 4 HOH A 68 568 62 HOH HOH . 
D 4 HOH A 69 569 55 HOH HOH . 
D 4 HOH A 70 570 39 HOH HOH . 
D 4 HOH A 71 571 38 HOH HOH . 
D 4 HOH A 72 572 69 HOH HOH . 
D 4 HOH A 73 573 63 HOH HOH . 
D 4 HOH A 74 574 75 HOH HOH . 
D 4 HOH A 75 575 67 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 AGS . . . B 2 26.749 -12.872 -1.409 1 127.23 ? PG AGS 401 A 1 
HETATM 2 S S1G AGS . . . B 2 26.486 -11.022 -0.845 1 127.34 ? S1G AGS 401 A 1 
HETATM 3 O O2G AGS . . . B 2 27.097 -12.902 -2.93 1 91.51 ? O2G AGS 401 A 1 
HETATM 4 O O3G AGS . . . B 2 25.41 -13.634 -1.185 1 168.79 ? O3G AGS 401 A 1 
HETATM 5 P PB AGS . . . B 2 28.642 -14.915 -0.87 1 30.5 ? PB AGS 401 A 1 
HETATM 6 O O1B AGS . . . B 2 28.617 -15.732 0.365 1 40.25 ? O1B AGS 401 A 1 
HETATM 7 O O2B AGS . . . B 2 27.958 -15.602 -2.067 1 33.22 ? O2B AGS 401 A 1 
HETATM 8 O O3B AGS . . . B 2 27.903 -13.515 -0.557 1 49.78 ? O3B AGS 401 A 1 
HETATM 9 P PA AGS . . . B 2 30.763 -15.042 -2.741 1 57.19 ? PA AGS 401 A 1 
HETATM 10 O O1A AGS . . . B 2 31.151 -16.477 -2.786 1 52.14 ? O1A AGS 401 A 1 
HETATM 11 O O2A AGS . . . B 2 29.738 -14.699 -3.827 1 76.36 ? O2A AGS 401 A 1 
HETATM 12 O O3A AGS . . . B 2 30.159 -14.614 -1.319 1 79.7 ? O3A AGS 401 A 1 
HETATM 13 O O5' AGS . . . B 2 32.043 -14.147 -3.008 1 68.9 ? O5' AGS 401 A 1 
HETATM 14 C C5' AGS . . . B 2 33.054 -13.773 -2.059 1 67.3 ? C5' AGS 401 A 1 
HETATM 15 C C4' AGS . . . B 2 34.252 -13.325 -2.865 1 74.05 ? C4' AGS 401 A 1 
HETATM 16 O O4' AGS . . . B 2 35.46 -13.794 -2.232 1 77.94 ? O4' AGS 401 A 1 
HETATM 17 C C3' AGS . . . B 2 34.327 -13.882 -4.28 1 69.92 ? C3' AGS 401 A 1 
HETATM 18 O O3' AGS . . . B 2 35.137 -13.052 -5.105 1 67.22 ? O3' AGS 401 A 1 
HETATM 19 C C2' AGS . . . B 2 34.978 -15.249 -4.054 1 72.88 ? C2' AGS 401 A 1 
HETATM 20 O O2' AGS . . . B 2 35.688 -15.715 -5.199 1 74.75 ? O2' AGS 401 A 1 
HETATM 21 C C1' AGS . . . B 2 35.929 -14.963 -2.884 1 71.8 ? C1' AGS 401 A 1 
HETATM 22 N N9 AGS . . . B 2 36.041 -16.03 -1.882 1 66.96 ? N9 AGS 401 A 1 
HETATM 23 C C8 AGS . . . B 2 35.209 -16.252 -0.816 1 61.43 ? C8 AGS 401 A 1 
HETATM 24 N N7 AGS . . . B 2 35.572 -17.258 -0.056 1 60.46 ? N7 AGS 401 A 1 
HETATM 25 C C5 AGS . . . B 2 36.734 -17.723 -0.66 1 62.25 ? C5 AGS 401 A 1 
HETATM 26 C C6 AGS . . . B 2 37.614 -18.777 -0.339 1 60.31 ? C6 AGS 401 A 1 
HETATM 27 N N6 AGS . . . B 2 37.456 -19.587 0.709 1 51.16 ? N6 AGS 401 A 1 
HETATM 28 N N1 AGS . . . B 2 38.679 -18.972 -1.151 1 63.49 ? N1 AGS 401 A 1 
HETATM 29 C C2 AGS . . . B 2 38.844 -18.165 -2.202 1 62.48 ? C2 AGS 401 A 1 
HETATM 30 N N3 AGS . . . B 2 38.084 -17.141 -2.598 1 61.53 ? N3 AGS 401 A 1 
HETATM 31 C C4 AGS . . . B 2 37.036 -16.971 -1.781 1 58.46 ? C4 AGS 401 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           292 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           31 
#