data_4Y9X # _model_server_result.job_id -vAn4ZIKDzMiFwWCYAaYUw _model_server_result.datetime_utc '2025-01-10 06:19:54' _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 4y9x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 4Y9X # _exptl.entry_id 4Y9X _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 186.057 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-PHOSPHOGLYCERIC ACID' _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 4Y9X _cell.length_a 98.85 _cell.length_b 98.85 _cell.length_c 127.79 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Y9X _symmetry.cell_setting ? _symmetry.Int_Tables_number 80 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 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 OD2 ASP 140 A ASP 136 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc2 A ND1 HIS 262 A HIS 258 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc3 B MN MN . A MN 401 1_555 E O1A UPG . A UPG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc4 B MN MN . A MN 401 1_555 E O2B UPG . A UPG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? metalc ? metalc5 B MN MN . A MN 401 1_555 I O HOH . A HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc6 B MN MN . A MN 401 1_555 I O HOH . A HOH 530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? # _chem_comp.formula 'C3 H7 O7 P' _chem_comp.formula_weight 186.057 _chem_comp.id 3PG _chem_comp.mon_nstd_flag . _chem_comp.name '3-PHOSPHOGLYCERIC ACID' _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 C1 O1 3PG doub 1 n n C1 O2 3PG sing 2 n n C1 C2 3PG sing 3 n n O2 HO2 3PG sing 4 n n C2 O3 3PG sing 5 n n C2 C3 3PG sing 6 n n C2 H2 3PG sing 7 n n O3 HO3 3PG sing 8 n n C3 O1P 3PG sing 9 n n C3 H31 3PG sing 10 n n C3 H32 3PG sing 11 n n O1P P 3PG sing 12 n n P O2P 3PG doub 13 n n P O3P 3PG sing 14 n n P O4P 3PG sing 15 n n O3P HOP3 3PG sing 16 n n O4P HOP4 3PG sing 17 n n # _atom_sites.entry_id 4Y9X _atom_sites.fract_transf_matrix[1][1] 0.010116 _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] 0.010116 _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] 0.007825 _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 MN A 1 401 1 MN MN . C 3 CL A 1 402 2 CL CL . D 4 3PG A 1 403 1 3PG 3PG . E 5 UPG A 1 404 2 UPG UPG . F 6 EDO A 1 405 4 EDO EDO . G 6 EDO A 1 406 5 EDO EDO . H 6 EDO A 1 407 1 EDO EDO . I 7 HOH A 1 501 46 HOH HOH . I 7 HOH A 2 502 53 HOH HOH . I 7 HOH A 3 503 73 HOH HOH . I 7 HOH A 4 504 36 HOH HOH . I 7 HOH A 5 505 84 HOH HOH . I 7 HOH A 6 506 88 HOH HOH . I 7 HOH A 7 507 8 HOH HOH . I 7 HOH A 8 508 1 HOH HOH . I 7 HOH A 9 509 2 HOH HOH . I 7 HOH A 10 510 3 HOH HOH . I 7 HOH A 11 511 5 HOH HOH . I 7 HOH A 12 512 6 HOH HOH . I 7 HOH A 13 513 7 HOH HOH . I 7 HOH A 14 514 9 HOH HOH . I 7 HOH A 15 515 10 HOH HOH . I 7 HOH A 16 516 11 HOH HOH . I 7 HOH A 17 517 12 HOH HOH . I 7 HOH A 18 518 13 HOH HOH . I 7 HOH A 19 519 14 HOH HOH . I 7 HOH A 20 520 15 HOH HOH . I 7 HOH A 21 521 16 HOH HOH . I 7 HOH A 22 522 17 HOH HOH . I 7 HOH A 23 523 18 HOH HOH . I 7 HOH A 24 524 20 HOH HOH . I 7 HOH A 25 525 23 HOH HOH . I 7 HOH A 26 526 24 HOH HOH . I 7 HOH A 27 527 26 HOH HOH . I 7 HOH A 28 528 29 HOH HOH . I 7 HOH A 29 529 30 HOH HOH . I 7 HOH A 30 530 32 HOH HOH . I 7 HOH A 31 531 34 HOH HOH . I 7 HOH A 32 532 35 HOH HOH . I 7 HOH A 33 533 37 HOH HOH . I 7 HOH A 34 534 38 HOH HOH . I 7 HOH A 35 535 39 HOH HOH . I 7 HOH A 36 536 40 HOH HOH . I 7 HOH A 37 537 41 HOH HOH . I 7 HOH A 38 538 42 HOH HOH . I 7 HOH A 39 539 44 HOH HOH . I 7 HOH A 40 540 50 HOH HOH . I 7 HOH A 41 541 51 HOH HOH . I 7 HOH A 42 542 52 HOH HOH . I 7 HOH A 43 543 54 HOH HOH . I 7 HOH A 44 544 56 HOH HOH . I 7 HOH A 45 545 59 HOH HOH . I 7 HOH A 46 546 60 HOH HOH . I 7 HOH A 47 547 61 HOH HOH . I 7 HOH A 48 548 62 HOH HOH . I 7 HOH A 49 549 64 HOH HOH . I 7 HOH A 50 550 65 HOH HOH . I 7 HOH A 51 551 66 HOH HOH . I 7 HOH A 52 552 67 HOH HOH . I 7 HOH A 53 553 68 HOH HOH . I 7 HOH A 54 554 69 HOH HOH . I 7 HOH A 55 555 70 HOH HOH . I 7 HOH A 56 556 71 HOH HOH . I 7 HOH A 57 557 74 HOH HOH . I 7 HOH A 58 558 75 HOH HOH . I 7 HOH A 59 559 79 HOH HOH . I 7 HOH A 60 560 81 HOH HOH . I 7 HOH A 61 561 82 HOH HOH . I 7 HOH A 62 562 83 HOH HOH . I 7 HOH A 63 563 85 HOH HOH . I 7 HOH A 64 564 86 HOH HOH . I 7 HOH A 65 565 87 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 3PG . . . D 4 8.67 -1.874 -28.609 1 104.8 ? C1 3PG 403 A 1 HETATM 2 O O1 3PG . . . D 4 9.924 -1.768 -28.561 1 103.62 ? O1 3PG 403 A 1 HETATM 3 O O2 3PG . . . D 4 7.954 -1.117 -27.906 1 92.28 ? O2 3PG 403 A 1 HETATM 4 C C2 3PG . . . D 4 8.021 -2.902 -29.511 1 109.38 ? C2 3PG 403 A 1 HETATM 5 O O3 3PG . . . D 4 9.005 -3.582 -30.256 1 105.83 ? O3 3PG 403 A 1 HETATM 6 C C3 3PG . . . D 4 7.07 -2.204 -30.455 1 106.39 ? C3 3PG 403 A 1 HETATM 7 O O1P 3PG . . . D 4 7.373 -2.566 -31.782 1 115.95 ? O1P 3PG 403 A 1 HETATM 8 P P 3PG . . . D 4 7.011 -1.546 -32.936 1 128.69 ? P 3PG 403 A 1 HETATM 9 O O2P 3PG . . . D 4 7.195 -2.213 -34.278 1 124.58 ? O2P 3PG 403 A 1 HETATM 10 O O3P 3PG . . . D 4 5.574 -1.103 -32.784 1 102.5 ? O3P 3PG 403 A 1 HETATM 11 O O4P 3PG . . . D 4 7.924 -0.347 -32.845 1 119.6 ? O4P 3PG 403 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 11 #