data_1JY8
#
_model_server_result.job_id            jrwKhZ4XcYvZT4tilaYOOg 
_model_server_result.datetime_utc      '2024-11-07 12:38:30' 
_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          1jy8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":421}' 
#
_entry.id    1JY8 
#
_exptl.entry_id    1JY8 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              278.091 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE' 
_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         90 
_cell.entry_id            1JY8 
_cell.length_a            144.63 
_cell.length_b            144.63 
_cell.length_c            144.63 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1JY8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        199 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'I 21 3' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 
3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_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 OD1 ASP 8 A ASP 8 1_555 B ZN ZN . A ZN 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? 
metalc ? metalc2 A NE2 HIS 10 A HIS 10 1_555 B ZN ZN . A ZN 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? 
metalc ? metalc3 A ND1 HIS 42 A HIS 42 1_555 B ZN ZN . A ZN 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? 
metalc ? metalc4 B ZN ZN . A ZN 300 1_555 D OA2 CDI . A CDI 421 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? 
#
_chem_comp.formula           'C5 H12 O9 P2' 
_chem_comp.formula_weight    278.091 
_chem_comp.id                CDI 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
C4 C3 CDI sing 106 n n 
C4 O2 CDI sing 107 n n 
C4 HC41 CDI sing 108 n n 
C4 HC42 CDI sing 109 n n 
C3 OB4 CDI sing 110 n n 
C3 C2 CDI sing 111 n n 
C3 C5 CDI sing 112 n n 
OB4 PB CDI sing 113 n n 
PB OB2 CDI sing 114 n n 
PB OB3 CDI doub 115 n n 
PB OB1 CDI sing 116 n n 
OB2 HB2O CDI sing 117 n n 
PA OA3 CDI sing 118 n n 
PA OA1 CDI sing 119 n n 
PA OA2 CDI doub 120 n n 
PA OB1 CDI sing 121 n n 
OA3 C1 CDI sing 122 n n 
OA1 HA1O CDI sing 123 n n 
C1 C2 CDI sing 124 n n 
C1 HC11 CDI sing 125 n n 
C1 HC12 CDI sing 126 n n 
C2 O1 CDI sing 127 n n 
C2 HC2 CDI sing 128 n n 
O1 HO1 CDI sing 129 n n 
C5 HC51 CDI sing 130 n n 
C5 HC52 CDI sing 131 n n 
C5 HC53 CDI sing 132 n n 
O2 HO2 CDI sing 133 n n 
#
_atom_sites.entry_id                     1JY8 
_atom_sites.fract_transf_matrix[1][1]    0.006914 
_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]    0.006914 
_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]    0.006914 
_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 ZN A 1 300 300 ZN ZN . 
C 3 C5P A 1 669 669 C5P CMP . 
D 4 CDI A 1 421 421 CDI CDI . 
E 5 HOH A 1 500 500 HOH SOL . 
E 5 HOH A 2 501 501 HOH SOL . 
E 5 HOH A 3 502 502 HOH SOL . 
E 5 HOH A 4 504 504 HOH SOL . 
E 5 HOH A 5 506 506 HOH SOL . 
E 5 HOH A 6 507 507 HOH SOL . 
E 5 HOH A 7 509 509 HOH SOL . 
E 5 HOH A 8 510 510 HOH SOL . 
E 5 HOH A 9 511 511 HOH SOL . 
E 5 HOH A 10 512 512 HOH SOL . 
E 5 HOH A 11 513 513 HOH SOL . 
E 5 HOH A 12 514 514 HOH SOL . 
E 5 HOH A 13 515 515 HOH SOL . 
E 5 HOH A 14 516 516 HOH SOL . 
E 5 HOH A 15 517 517 HOH SOL . 
E 5 HOH A 16 518 518 HOH SOL . 
E 5 HOH A 17 519 519 HOH SOL . 
E 5 HOH A 18 520 520 HOH SOL . 
E 5 HOH A 19 521 521 HOH SOL . 
E 5 HOH A 20 523 523 HOH SOL . 
E 5 HOH A 21 524 524 HOH SOL . 
E 5 HOH A 22 525 525 HOH SOL . 
E 5 HOH A 23 526 526 HOH SOL . 
E 5 HOH A 24 527 527 HOH SOL . 
E 5 HOH A 25 528 528 HOH SOL . 
E 5 HOH A 26 529 529 HOH SOL . 
E 5 HOH A 27 530 530 HOH SOL . 
E 5 HOH A 28 531 531 HOH SOL . 
E 5 HOH A 29 532 532 HOH SOL . 
E 5 HOH A 30 533 533 HOH SOL . 
E 5 HOH A 31 535 535 HOH SOL . 
E 5 HOH A 32 536 536 HOH SOL . 
E 5 HOH A 33 537 537 HOH SOL . 
E 5 HOH A 34 538 538 HOH SOL . 
E 5 HOH A 35 539 539 HOH SOL . 
E 5 HOH A 36 540 540 HOH SOL . 
E 5 HOH A 37 541 541 HOH SOL . 
E 5 HOH A 38 542 542 HOH SOL . 
E 5 HOH A 39 543 543 HOH SOL . 
E 5 HOH A 40 545 545 HOH SOL . 
E 5 HOH A 41 546 546 HOH SOL . 
E 5 HOH A 42 547 547 HOH SOL . 
E 5 HOH A 43 549 549 HOH SOL . 
E 5 HOH A 44 550 550 HOH SOL . 
E 5 HOH A 45 551 551 HOH SOL . 
E 5 HOH A 46 554 554 HOH SOL . 
E 5 HOH A 47 555 555 HOH SOL . 
E 5 HOH A 48 556 556 HOH SOL . 
E 5 HOH A 49 557 557 HOH SOL . 
E 5 HOH A 50 558 558 HOH SOL . 
E 5 HOH A 51 560 560 HOH SOL . 
E 5 HOH A 52 561 561 HOH SOL . 
E 5 HOH A 53 563 563 HOH SOL . 
E 5 HOH A 54 564 564 HOH SOL . 
E 5 HOH A 55 568 568 HOH SOL . 
E 5 HOH A 56 571 571 HOH SOL . 
E 5 HOH A 57 573 573 HOH SOL . 
E 5 HOH A 58 574 574 HOH SOL . 
E 5 HOH A 59 575 575 HOH SOL . 
E 5 HOH A 60 576 576 HOH SOL . 
E 5 HOH A 61 579 579 HOH SOL . 
E 5 HOH A 62 580 580 HOH SOL . 
E 5 HOH A 63 581 581 HOH SOL . 
E 5 HOH A 64 582 582 HOH SOL . 
E 5 HOH A 65 583 583 HOH SOL . 
E 5 HOH A 66 584 584 HOH SOL . 
E 5 HOH A 67 585 585 HOH SOL . 
E 5 HOH A 68 586 586 HOH SOL . 
E 5 HOH A 69 588 588 HOH SOL . 
E 5 HOH A 70 589 589 HOH SOL . 
E 5 HOH A 71 590 590 HOH SOL . 
E 5 HOH A 72 592 592 HOH SOL . 
#
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 C C4 CDI . . . D 4 16.179 34.225 4.344 1 47.78 ? C4 CDI 421 A 1 
HETATM 2 C C3 CDI . . . D 4 16.103 33.048 5.368 1 48.15 ? C3 CDI 421 A 1 
HETATM 3 O OB4 CDI . . . D 4 15.382 31.95 4.735 1 48.37 ? OB4 CDI 421 A 1 
HETATM 4 P PB CDI . . . D 4 15.625 30.46 4.134 1 50.49 ? PB CDI 421 A 1 
HETATM 5 O OB2 CDI . . . D 4 14.275 29.852 3.563 1 48.89 ? OB2 CDI 421 A 1 
HETATM 6 O OB3 CDI . . . D 4 16.756 30.457 2.987 1 45.72 ? OB3 CDI 421 A 1 
HETATM 7 P PA CDI . . . D 4 14.965 29.544 6.563 1 41.22 ? PA CDI 421 A 1 
HETATM 8 O OA3 CDI . . . D 4 14.553 30.965 7.209 1 46.68 ? OA3 CDI 421 A 1 
HETATM 9 O OA1 CDI . . . D 4 13.7 28.652 6.256 1 42.46 ? OA1 CDI 421 A 1 
HETATM 10 O OA2 CDI . . . D 4 15.975 28.721 7.472 1 36.91 ? OA2 CDI 421 A 1 
HETATM 11 C C1 CDI . . . D 4 15.145 32.203 7.707 1 47.75 ? C1 CDI 421 A 1 
HETATM 12 C C2 CDI . . . D 4 15.276 33.377 6.663 1 47.14 ? C2 CDI 421 A 1 
HETATM 13 O O1 CDI . . . D 4 15.876 34.454 7.389 1 50.89 ? O1 CDI 421 A 1 
HETATM 14 C C5 CDI . . . D 4 17.558 32.653 5.753 1 46.72 ? C5 CDI 421 A 1 
HETATM 15 O O2 CDI . . . D 4 14.865 34.645 3.953 1 48.42 ? O2 CDI 421 A 1 
HETATM 16 O OB1 CDI . . . D 4 15.693 29.403 5.246 1 49.24 ? OB1 CDI 421 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           304 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           16 
#