data_6JDI
#
_model_server_result.job_id            Dw-WzRiwUjt6nPTznnsTiw 
_model_server_result.datetime_utc      '2024-10-18 16:27:14' 
_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          6jdi 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":401}' 
#
_entry.id    6JDI 
#
_exptl.entry_id    6JDI 
_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            6JDI 
_cell.length_a            105.065 
_cell.length_b            105.065 
_cell.length_c            42.642 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6JDI 
_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 ? ? ? ? ? ? ? ? ? ? ? ? 2.972 ? 
metalc ? metalc2 B O2G AGS . A AGS 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? 
metalc ? metalc3 C MG MG . A MG 402 1_555 D O HOH . A HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? 
metalc ? metalc4 C MG MG . A MG 402 1_555 D O HOH . A HOH 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? 
metalc ? metalc5 C MG MG . A MG 402 1_555 D O HOH . A HOH 543 5_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? 
#
_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                     6JDI 
_atom_sites.fract_transf_matrix[1][1]    0.009518 
_atom_sites.fract_transf_matrix[1][2]    0.005495 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01099 
_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]    0.023451 
_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 97 HOH HOH . 
D 4 HOH A 2 502 42 HOH HOH . 
D 4 HOH A 3 503 100 HOH HOH . 
D 4 HOH A 4 504 76 HOH HOH . 
D 4 HOH A 5 505 65 HOH HOH . 
D 4 HOH A 6 506 4 HOH HOH . 
D 4 HOH A 7 507 32 HOH HOH . 
D 4 HOH A 8 508 105 HOH HOH . 
D 4 HOH A 9 509 13 HOH HOH . 
D 4 HOH A 10 510 79 HOH HOH . 
D 4 HOH A 11 511 106 HOH HOH . 
D 4 HOH A 12 512 70 HOH HOH . 
D 4 HOH A 13 513 3 HOH HOH . 
D 4 HOH A 14 514 46 HOH HOH . 
D 4 HOH A 15 515 44 HOH HOH . 
D 4 HOH A 16 516 89 HOH HOH . 
D 4 HOH A 17 517 38 HOH HOH . 
D 4 HOH A 18 518 83 HOH HOH . 
D 4 HOH A 19 519 25 HOH HOH . 
D 4 HOH A 20 520 19 HOH HOH . 
D 4 HOH A 21 521 16 HOH HOH . 
D 4 HOH A 22 522 21 HOH HOH . 
D 4 HOH A 23 523 53 HOH HOH . 
D 4 HOH A 24 524 37 HOH HOH . 
D 4 HOH A 25 525 11 HOH HOH . 
D 4 HOH A 26 526 10 HOH HOH . 
D 4 HOH A 27 527 71 HOH HOH . 
D 4 HOH A 28 528 36 HOH HOH . 
D 4 HOH A 29 529 2 HOH HOH . 
D 4 HOH A 30 530 101 HOH HOH . 
D 4 HOH A 31 531 48 HOH HOH . 
D 4 HOH A 32 532 33 HOH HOH . 
D 4 HOH A 33 533 87 HOH HOH . 
D 4 HOH A 34 534 73 HOH HOH . 
D 4 HOH A 35 535 12 HOH HOH . 
D 4 HOH A 36 536 47 HOH HOH . 
D 4 HOH A 37 537 49 HOH HOH . 
D 4 HOH A 38 538 95 HOH HOH . 
D 4 HOH A 39 539 85 HOH HOH . 
D 4 HOH A 40 540 51 HOH HOH . 
D 4 HOH A 41 541 7 HOH HOH . 
D 4 HOH A 42 542 35 HOH HOH . 
D 4 HOH A 43 543 17 HOH HOH . 
D 4 HOH A 44 544 5 HOH HOH . 
D 4 HOH A 45 545 26 HOH HOH . 
D 4 HOH A 46 546 92 HOH HOH . 
D 4 HOH A 47 547 20 HOH HOH . 
D 4 HOH A 48 548 96 HOH HOH . 
D 4 HOH A 49 549 61 HOH HOH . 
D 4 HOH A 50 550 86 HOH HOH . 
D 4 HOH A 51 551 104 HOH HOH . 
D 4 HOH A 52 552 8 HOH HOH . 
D 4 HOH A 53 553 77 HOH HOH . 
D 4 HOH A 54 554 24 HOH HOH . 
D 4 HOH A 55 555 103 HOH HOH . 
D 4 HOH A 56 556 69 HOH HOH . 
D 4 HOH A 57 557 43 HOH HOH . 
D 4 HOH A 58 558 82 HOH HOH . 
D 4 HOH A 59 559 15 HOH HOH . 
D 4 HOH A 60 560 74 HOH HOH . 
D 4 HOH A 61 561 52 HOH HOH . 
D 4 HOH A 62 562 39 HOH HOH . 
D 4 HOH A 63 563 23 HOH HOH . 
D 4 HOH A 64 564 34 HOH HOH . 
D 4 HOH A 65 565 62 HOH HOH . 
D 4 HOH A 66 566 28 HOH HOH . 
D 4 HOH A 67 567 94 HOH HOH . 
D 4 HOH A 68 568 9 HOH HOH . 
D 4 HOH A 69 569 22 HOH HOH . 
D 4 HOH A 70 570 27 HOH HOH . 
D 4 HOH A 71 571 59 HOH HOH . 
D 4 HOH A 72 572 80 HOH HOH . 
D 4 HOH A 73 573 55 HOH HOH . 
D 4 HOH A 74 574 31 HOH HOH . 
D 4 HOH A 75 575 99 HOH HOH . 
D 4 HOH A 76 576 29 HOH HOH . 
D 4 HOH A 77 577 57 HOH HOH . 
D 4 HOH A 78 578 30 HOH HOH . 
D 4 HOH A 79 579 6 HOH HOH . 
D 4 HOH A 80 580 18 HOH HOH . 
D 4 HOH A 81 581 54 HOH HOH . 
D 4 HOH A 82 582 107 HOH HOH . 
D 4 HOH A 83 583 64 HOH HOH . 
D 4 HOH A 84 584 78 HOH HOH . 
D 4 HOH A 85 585 67 HOH HOH . 
D 4 HOH A 86 586 50 HOH HOH . 
D 4 HOH A 87 587 40 HOH HOH . 
D 4 HOH A 88 588 45 HOH HOH . 
D 4 HOH A 89 589 58 HOH HOH . 
D 4 HOH A 90 590 66 HOH HOH . 
D 4 HOH A 91 591 63 HOH HOH . 
D 4 HOH A 92 592 56 HOH HOH . 
D 4 HOH A 93 593 84 HOH HOH . 
D 4 HOH A 94 594 102 HOH HOH . 
D 4 HOH A 95 595 91 HOH HOH . 
D 4 HOH A 96 596 1 HOH HOH . 
D 4 HOH A 97 597 88 HOH HOH . 
D 4 HOH A 98 598 68 HOH HOH . 
D 4 HOH A 99 599 41 HOH HOH . 
D 4 HOH A 100 600 98 HOH HOH . 
D 4 HOH A 101 601 81 HOH HOH . 
D 4 HOH A 102 602 90 HOH HOH . 
D 4 HOH A 103 603 14 HOH HOH . 
D 4 HOH A 104 604 93 HOH HOH . 
D 4 HOH A 105 605 60 HOH HOH . 
D 4 HOH A 106 606 75 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 -26.92 -12.949 -2.864 1 90.46 ? PG AGS 401 A 1 
HETATM 2 S S1G AGS . . . B 2 -27.051 -11.08 -3.398 1 77.3 ? S1G AGS 401 A 1 
HETATM 3 O O2G AGS . . . B 2 -27.027 -13.072 -1.317 1 66.46 ? O2G AGS 401 A 1 
HETATM 4 O O3G AGS . . . B 2 -25.547 -13.518 -3.319 1 98.59 ? O3G AGS 401 A 1 
HETATM 5 P PB AGS . . . B 2 -28.689 -15.104 -3.23 1 33.82 ? PB AGS 401 A 1 
HETATM 6 O O1B AGS . . . B 2 -28.685 -15.883 -4.477 1 28.95 ? O1B AGS 401 A 1 
HETATM 7 O O2B AGS . . . B 2 -27.935 -15.801 -2.091 1 30.71 ? O2B AGS 401 A 1 
HETATM 8 O O3B AGS . . . B 2 -28.08 -13.691 -3.597 1 43.99 ? O3B AGS 401 A 1 
HETATM 9 P PA AGS . . . B 2 -31.02 -15.143 -1.488 1 39.56 ? PA AGS 401 A 1 
HETATM 10 O O1A AGS . . . B 2 -31.015 -16.611 -1.286 1 31.43 ? O1A AGS 401 A 1 
HETATM 11 O O2A AGS . . . B 2 -30.561 -14.321 -0.282 1 47.47 ? O2A AGS 401 A 1 
HETATM 12 O O3A AGS . . . B 2 -30.202 -14.755 -2.799 1 46.28 ? O3A AGS 401 A 1 
HETATM 13 O O5' AGS . . . B 2 -32.519 -14.71 -1.898 1 44.8 ? O5' AGS 401 A 1 
HETATM 14 C C5' AGS . . . B 2 -32.97 -13.315 -1.896 1 39.58 ? C5' AGS 401 A 1 
HETATM 15 C C4' AGS . . . B 2 -34.332 -13.218 -1.239 1 42.18 ? C4' AGS 401 A 1 
HETATM 16 O O4' AGS . . . B 2 -35.326 -13.873 -2.06 1 44.86 ? O4' AGS 401 A 1 
HETATM 17 C C3' AGS . . . B 2 -34.446 -13.86 0.139 1 50.59 ? C3' AGS 401 A 1 
HETATM 18 O O3' AGS . . . B 2 -35.311 -13.086 0.963 1 49.76 ? O3' AGS 401 A 1 
HETATM 19 C C2' AGS . . . B 2 -34.997 -15.258 -0.176 1 48.5 ? C2' AGS 401 A 1 
HETATM 20 O O2' AGS . . . B 2 -35.793 -15.772 0.883 1 44.06 ? O2' AGS 401 A 1 
HETATM 21 C C1' AGS . . . B 2 -35.881 -14.989 -1.391 1 41 ? C1' AGS 401 A 1 
HETATM 22 N N9 AGS . . . B 2 -36.005 -16.079 -2.356 1 43.7 ? N9 AGS 401 A 1 
HETATM 23 C C8 AGS . . . B 2 -35.166 -16.34 -3.409 1 39.07 ? C8 AGS 401 A 1 
HETATM 24 N N7 AGS . . . B 2 -35.543 -17.348 -4.16 1 42.04 ? N7 AGS 401 A 1 
HETATM 25 C C5 AGS . . . B 2 -36.719 -17.776 -3.565 1 45.97 ? C5 AGS 401 A 1 
HETATM 26 C C6 AGS . . . B 2 -37.623 -18.812 -3.883 1 44.23 ? C6 AGS 401 A 1 
HETATM 27 N N6 AGS . . . B 2 -37.467 -19.641 -4.916 1 43.11 ? N6 AGS 401 A 1 
HETATM 28 N N1 AGS . . . B 2 -38.703 -18.968 -3.09 1 49.22 ? N1 AGS 401 A 1 
HETATM 29 C C2 AGS . . . B 2 -38.868 -18.139 -2.059 1 48.18 ? C2 AGS 401 A 1 
HETATM 30 N N3 AGS . . . B 2 -38.089 -17.13 -1.664 1 41.75 ? N3 AGS 401 A 1 
HETATM 31 C C4 AGS . . . B 2 -37.025 -17 -2.462 1 46.6 ? C4 AGS 401 A 1 
#
_model_server_stats.io_time_ms              67 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           234 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           31 
#