data_5KPT
#
_model_server_result.job_id            buXkrxObQ1UQUxWV5MsjGQ 
_model_server_result.datetime_utc      '2024-10-11 13:27:09' 
_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          5kpt 
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_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":403}' 
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_entry.id    5KPT 
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_exptl.entry_id    5KPT 
_exptl.method      'X-RAY DIFFRACTION' 
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_entity.details                     ? 
_entity.formula_weight              62.068 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1,2-ETHANEDIOL 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
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_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         120 
_cell.entry_id            5KPT 
_cell.length_a            97.463 
_cell.length_b            97.463 
_cell.length_c            68.161 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
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_symmetry.entry_id                 5KPT 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31 2 1' 
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_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
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_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 
#
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' 6_554 -x,-x+y,-z-2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 -45.440667 
#
_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 B MG MG . A MG 401 1_555 C O3G ANP . A ANP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? 
metalc ? metalc2 B MG MG . A MG 401 1_555 C O2B ANP . A ANP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.9 ? 
metalc ? metalc3 B MG MG . A MG 401 1_555 E O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
metalc ? metalc4 B MG MG . A MG 401 1_555 E O HOH . A HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? 
metalc ? metalc5 B MG MG . A MG 401 1_555 E O HOH . A HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? 
metalc ? metalc6 B MG MG . A MG 401 1_555 E O HOH . A HOH 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? 
#
_chem_comp.formula           'C2 H6 O2' 
_chem_comp.formula_weight    62.068 
_chem_comp.id                EDO 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1,2-ETHANEDIOL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'ETHYLENE GLYCOL' 
#
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
C1 O1 EDO sing 133 n n 
C1 C2 EDO sing 134 n n 
C1 H11 EDO sing 135 n n 
C1 H12 EDO sing 136 n n 
O1 HO1 EDO sing 137 n n 
C2 O2 EDO sing 138 n n 
C2 H21 EDO sing 139 n n 
C2 H22 EDO sing 140 n n 
O2 HO2 EDO sing 141 n n 
#
_atom_sites.entry_id                     5KPT 
_atom_sites.fract_transf_matrix[1][1]    0.01026 
_atom_sites.fract_transf_matrix[1][2]    0.005924 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011848 
_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]    0.014671 
_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 MG A 1 401 1 MG MG . 
C 3 ANP A 1 402 501 ANP ANP . 
D 4 EDO A 1 403 1 EDO EDO . 
E 5 HOH A 1 501 28 HOH HOH . 
E 5 HOH A 2 502 2 HOH HOH . 
E 5 HOH A 3 503 72 HOH HOH . 
E 5 HOH A 4 504 1 HOH HOH . 
E 5 HOH A 5 505 10 HOH HOH . 
E 5 HOH A 6 506 22 HOH HOH . 
E 5 HOH A 7 507 3 HOH HOH . 
E 5 HOH A 8 508 53 HOH HOH . 
E 5 HOH A 9 509 33 HOH HOH . 
E 5 HOH A 10 510 56 HOH HOH . 
E 5 HOH A 11 511 5 HOH HOH . 
E 5 HOH A 12 512 71 HOH HOH . 
E 5 HOH A 13 513 12 HOH HOH . 
E 5 HOH A 14 514 25 HOH HOH . 
E 5 HOH A 15 515 98 HOH HOH . 
E 5 HOH A 16 516 48 HOH HOH . 
E 5 HOH A 17 517 26 HOH HOH . 
E 5 HOH A 18 518 51 HOH HOH . 
E 5 HOH A 19 519 17 HOH HOH . 
E 5 HOH A 20 520 34 HOH HOH . 
E 5 HOH A 21 521 44 HOH HOH . 
E 5 HOH A 22 522 81 HOH HOH . 
E 5 HOH A 23 523 52 HOH HOH . 
E 5 HOH A 24 524 88 HOH HOH . 
E 5 HOH A 25 525 4 HOH HOH . 
E 5 HOH A 26 526 20 HOH HOH . 
E 5 HOH A 27 527 31 HOH HOH . 
E 5 HOH A 28 528 11 HOH HOH . 
E 5 HOH A 29 529 42 HOH HOH . 
E 5 HOH A 30 530 35 HOH HOH . 
E 5 HOH A 31 531 47 HOH HOH . 
E 5 HOH A 32 532 55 HOH HOH . 
E 5 HOH A 33 533 54 HOH HOH . 
E 5 HOH A 34 534 50 HOH HOH . 
E 5 HOH A 35 535 21 HOH HOH . 
E 5 HOH A 36 536 63 HOH HOH . 
E 5 HOH A 37 537 68 HOH HOH . 
E 5 HOH A 38 538 36 HOH HOH . 
E 5 HOH A 39 539 49 HOH HOH . 
E 5 HOH A 40 540 95 HOH HOH . 
E 5 HOH A 41 541 45 HOH HOH . 
E 5 HOH A 42 542 30 HOH HOH . 
E 5 HOH A 43 543 86 HOH HOH . 
E 5 HOH A 44 544 57 HOH HOH . 
E 5 HOH A 45 545 69 HOH HOH . 
E 5 HOH A 46 546 19 HOH HOH . 
E 5 HOH A 47 547 85 HOH HOH . 
E 5 HOH A 48 548 43 HOH HOH . 
E 5 HOH A 49 549 84 HOH HOH . 
E 5 HOH A 50 550 87 HOH HOH . 
E 5 HOH A 51 551 32 HOH HOH . 
E 5 HOH A 52 552 9 HOH HOH . 
E 5 HOH A 53 553 15 HOH HOH . 
E 5 HOH A 54 554 82 HOH HOH . 
E 5 HOH A 55 555 96 HOH HOH . 
E 5 HOH A 56 556 83 HOH HOH . 
E 5 HOH A 57 557 80 HOH HOH . 
E 5 HOH A 58 558 89 HOH HOH . 
E 5 HOH A 59 559 77 HOH HOH . 
E 5 HOH A 60 560 79 HOH HOH . 
E 5 HOH A 61 561 65 HOH HOH . 
E 5 HOH A 62 562 97 HOH HOH . 
E 5 HOH A 63 563 14 HOH HOH . 
E 5 HOH A 64 564 92 HOH HOH . 
E 5 HOH A 65 565 8 HOH HOH . 
E 5 HOH A 66 566 13 HOH HOH . 
E 5 HOH A 67 567 99 HOH HOH . 
E 5 HOH A 68 568 93 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 C C1 EDO . . . D 4 -26.029 21.681 -13.423 1 34.99 ? C1 EDO 403 A 1 
HETATM 2 O O1 EDO . . . D 4 -27.312 21.041 -13.444 1 45.17 ? O1 EDO 403 A 1 
HETATM 3 C C2 EDO . . . D 4 -25.393 21.518 -14.8 1 38.78 ? C2 EDO 403 A 1 
HETATM 4 O O2 EDO . . . D 4 -24.623 20.309 -14.818 1 41.6 ? O2 EDO 403 A 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           336 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           4 
#