data_5GW8 # _model_server_result.job_id kq387uYTlhZg8sy1LRVwXg _model_server_result.datetime_utc '2024-11-27 19:52:18' _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 5gw8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":405}' # _entry.id 5GW8 # _exptl.entry_id 5GW8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 104.061 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MALONIC ACID' _entity.pdbx_number_of_molecules 2 _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 5GW8 _cell.length_a 76.97 _cell.length_b 82.32 _cell.length_c 116.87 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GW8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 K N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C NAG 1 C 1 NAG C 2 NAG 2 n C NAG 2 C 2 NAG C 3 NAG 2 n D NAG 1 D 1 NAG C 5 NAG 2 n D NAG 2 D 2 NAG C 6 NAG # 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 disulf ? disulf1 A SG CYS 37 A CYS 55 1_555 A SG CYS 279 A CYS 297 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf2 B SG CYS 37 B CYS 55 1_555 B SG CYS 279 B CYS 297 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? covale ? covale1 A ND2 ASN 84 A ASN 102 1_555 E C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale2 A ND2 ASN 235 A ASN 253 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale3 B ND2 ASN 84 B ASN 102 1_555 I C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale4 B ND2 ASN 235 B ASN 253 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale6 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? # _chem_comp.formula 'C3 H4 O4' _chem_comp.formula_weight 104.061 _chem_comp.id MLA _chem_comp.mon_nstd_flag . _chem_comp.name 'MALONIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'DICARBOXYLIC ACID C3;PROPANEDIOLIC ACID;METHANEDICARBOXYLIC ACID' # 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 O1A MLA sing 261 n n C1 O1B MLA doub 262 n n C1 C2 MLA sing 263 n n O1A H1A MLA sing 264 n n C2 C3 MLA sing 265 n n C2 HC21 MLA sing 266 n n C2 HC22 MLA sing 267 n n C3 O3A MLA doub 268 n n C3 O3B MLA sing 269 n n O3B H3B MLA sing 270 n n # _atom_sites.entry_id 5GW8 _atom_sites.fract_transf_matrix[1][1] 0.012992 _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] 0.012148 _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] 0.008557 _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 E 3 NAG A 1 401 1 NAG NAG . F 4 MLA A 1 404 1 MLA MLA . G 5 ACY A 1 405 1 ACY ACY . H 6 FMT A 1 406 2 FMT FMT . I 3 NAG B 1 401 4 NAG NAG . J 7 GOL B 1 404 1 GOL GOL . K 4 MLA B 1 405 2 MLA MLA . L 5 ACY B 1 406 2 ACY ACY . M 5 ACY B 1 407 3 ACY ACY . N 5 ACY B 1 408 4 ACY ACY . O 6 FMT B 1 409 3 FMT FMT . P 8 HOH A 1 501 45 HOH HOH . P 8 HOH A 2 502 8 HOH HOH . P 8 HOH A 3 503 26 HOH HOH . P 8 HOH A 4 504 196 HOH HOH . P 8 HOH A 5 505 1 HOH HOH . P 8 HOH A 6 506 46 HOH HOH . P 8 HOH A 7 507 179 HOH HOH . P 8 HOH A 8 508 12 HOH HOH . P 8 HOH A 9 509 157 HOH HOH . P 8 HOH A 10 510 11 HOH HOH . P 8 HOH A 11 511 85 HOH HOH . P 8 HOH A 12 512 47 HOH HOH . P 8 HOH A 13 513 33 HOH HOH . P 8 HOH A 14 514 6 HOH HOH . P 8 HOH A 15 515 124 HOH HOH . P 8 HOH A 16 516 35 HOH HOH . P 8 HOH A 17 517 191 HOH HOH . P 8 HOH A 18 518 23 HOH HOH . P 8 HOH A 19 519 99 HOH HOH . P 8 HOH A 20 520 2 HOH HOH . P 8 HOH A 21 521 17 HOH HOH . P 8 HOH A 22 522 169 HOH HOH . P 8 HOH A 23 523 149 HOH HOH . P 8 HOH A 24 524 4 HOH HOH . P 8 HOH A 25 525 105 HOH HOH . P 8 HOH A 26 526 127 HOH HOH . P 8 HOH A 27 527 187 HOH HOH . P 8 HOH A 28 528 153 HOH HOH . P 8 HOH A 29 529 193 HOH HOH . P 8 HOH A 30 530 34 HOH HOH . P 8 HOH A 31 531 102 HOH HOH . P 8 HOH A 32 532 184 HOH HOH . P 8 HOH A 33 533 131 HOH HOH . P 8 HOH A 34 534 92 HOH HOH . P 8 HOH A 35 535 7 HOH HOH . P 8 HOH A 36 536 27 HOH HOH . P 8 HOH A 37 537 37 HOH HOH . P 8 HOH A 38 538 160 HOH HOH . P 8 HOH A 39 539 5 HOH HOH . P 8 HOH A 40 540 20 HOH HOH . P 8 HOH A 41 541 97 HOH HOH . P 8 HOH A 42 542 130 HOH HOH . P 8 HOH A 43 543 19 HOH HOH . P 8 HOH A 44 544 150 HOH HOH . P 8 HOH A 45 545 180 HOH HOH . P 8 HOH A 46 546 188 HOH HOH . P 8 HOH A 47 547 168 HOH HOH . P 8 HOH A 48 548 148 HOH HOH . P 8 HOH A 49 549 24 HOH HOH . P 8 HOH A 50 550 15 HOH HOH . P 8 HOH A 51 551 154 HOH HOH . P 8 HOH A 52 552 104 HOH HOH . P 8 HOH A 53 553 14 HOH HOH . P 8 HOH A 54 554 32 HOH HOH . P 8 HOH A 55 555 158 HOH HOH . P 8 HOH A 56 556 36 HOH HOH . P 8 HOH A 57 557 31 HOH HOH . P 8 HOH A 58 558 10 HOH HOH . P 8 HOH A 59 559 164 HOH HOH . P 8 HOH A 60 560 16 HOH HOH . P 8 HOH A 61 561 86 HOH HOH . P 8 HOH A 62 562 30 HOH HOH . P 8 HOH A 63 563 126 HOH HOH . P 8 HOH A 64 564 103 HOH HOH . P 8 HOH A 65 565 13 HOH HOH . P 8 HOH A 66 566 151 HOH HOH . P 8 HOH A 67 567 125 HOH HOH . P 8 HOH A 68 568 96 HOH HOH . P 8 HOH A 69 569 18 HOH HOH . P 8 HOH A 70 570 28 HOH HOH . P 8 HOH A 71 571 21 HOH HOH . P 8 HOH A 72 572 3 HOH HOH . P 8 HOH A 73 573 25 HOH HOH . P 8 HOH A 74 574 129 HOH HOH . P 8 HOH A 75 575 128 HOH HOH . P 8 HOH A 76 576 95 HOH HOH . P 8 HOH A 77 577 122 HOH HOH . P 8 HOH A 78 578 22 HOH HOH . P 8 HOH A 79 579 100 HOH HOH . P 8 HOH A 80 580 170 HOH HOH . P 8 HOH A 81 581 101 HOH HOH . P 8 HOH A 82 582 94 HOH HOH . P 8 HOH A 83 583 156 HOH HOH . P 8 HOH A 84 584 159 HOH HOH . P 8 HOH A 85 585 185 HOH HOH . P 8 HOH A 86 586 186 HOH HOH . Q 8 HOH B 1 501 172 HOH HOH . Q 8 HOH B 2 502 111 HOH HOH . Q 8 HOH B 3 503 56 HOH HOH . Q 8 HOH B 4 504 74 HOH HOH . Q 8 HOH B 5 505 89 HOH HOH . Q 8 HOH B 6 506 40 HOH HOH . Q 8 HOH B 7 507 137 HOH HOH . Q 8 HOH B 8 508 42 HOH HOH . Q 8 HOH B 9 509 119 HOH HOH . Q 8 HOH B 10 510 197 HOH HOH . Q 8 HOH B 11 511 177 HOH HOH . Q 8 HOH B 12 512 113 HOH HOH . Q 8 HOH B 13 513 140 HOH HOH . Q 8 HOH B 14 514 133 HOH HOH . Q 8 HOH B 15 515 141 HOH HOH . Q 8 HOH B 16 516 84 HOH HOH . Q 8 HOH B 17 517 121 HOH HOH . Q 8 HOH B 18 518 53 HOH HOH . Q 8 HOH B 19 519 171 HOH HOH . Q 8 HOH B 20 520 73 HOH HOH . Q 8 HOH B 21 521 41 HOH HOH . Q 8 HOH B 22 522 194 HOH HOH . Q 8 HOH B 23 523 52 HOH HOH . Q 8 HOH B 24 524 51 HOH HOH . Q 8 HOH B 25 525 165 HOH HOH . Q 8 HOH B 26 526 67 HOH HOH . Q 8 HOH B 27 527 135 HOH HOH . Q 8 HOH B 28 528 138 HOH HOH . Q 8 HOH B 29 529 50 HOH HOH . Q 8 HOH B 30 530 139 HOH HOH . Q 8 HOH B 31 531 176 HOH HOH . Q 8 HOH B 32 532 71 HOH HOH . Q 8 HOH B 33 533 181 HOH HOH . Q 8 HOH B 34 534 143 HOH HOH . Q 8 HOH B 35 535 167 HOH HOH . Q 8 HOH B 36 536 72 HOH HOH . Q 8 HOH B 37 537 79 HOH HOH . Q 8 HOH B 38 538 38 HOH HOH . Q 8 HOH B 39 539 57 HOH HOH . Q 8 HOH B 40 540 39 HOH HOH . Q 8 HOH B 41 541 65 HOH HOH . Q 8 HOH B 42 542 49 HOH HOH . Q 8 HOH B 43 543 62 HOH HOH . Q 8 HOH B 44 544 146 HOH HOH . Q 8 HOH B 45 545 81 HOH HOH . Q 8 HOH B 46 546 69 HOH HOH . Q 8 HOH B 47 547 147 HOH HOH . Q 8 HOH B 48 548 134 HOH HOH . Q 8 HOH B 49 549 54 HOH HOH . Q 8 HOH B 50 550 60 HOH HOH . Q 8 HOH B 51 551 29 HOH HOH . Q 8 HOH B 52 552 77 HOH HOH . Q 8 HOH B 53 553 118 HOH HOH . Q 8 HOH B 54 554 76 HOH HOH . Q 8 HOH B 55 555 90 HOH HOH . Q 8 HOH B 56 556 80 HOH HOH . Q 8 HOH B 57 557 82 HOH HOH . Q 8 HOH B 58 558 66 HOH HOH . Q 8 HOH B 59 559 78 HOH HOH . Q 8 HOH B 60 560 64 HOH HOH . Q 8 HOH B 61 561 106 HOH HOH . Q 8 HOH B 62 562 136 HOH HOH . Q 8 HOH B 63 563 48 HOH HOH . Q 8 HOH B 64 564 120 HOH HOH . Q 8 HOH B 65 565 63 HOH HOH . Q 8 HOH B 66 566 44 HOH HOH . Q 8 HOH B 67 567 107 HOH HOH . Q 8 HOH B 68 568 59 HOH HOH . Q 8 HOH B 69 569 195 HOH HOH . Q 8 HOH B 70 570 75 HOH HOH . Q 8 HOH B 71 571 163 HOH HOH . Q 8 HOH B 72 572 161 HOH HOH . Q 8 HOH B 73 573 117 HOH HOH . Q 8 HOH B 74 574 98 HOH HOH . Q 8 HOH B 75 575 108 HOH HOH . Q 8 HOH B 76 576 43 HOH HOH . Q 8 HOH B 77 577 93 HOH HOH . Q 8 HOH B 78 578 83 HOH HOH . Q 8 HOH B 79 579 70 HOH HOH . Q 8 HOH B 80 580 55 HOH HOH . Q 8 HOH B 81 581 109 HOH HOH . Q 8 HOH B 82 582 174 HOH HOH . Q 8 HOH B 83 583 192 HOH HOH . Q 8 HOH B 84 584 58 HOH HOH . Q 8 HOH B 85 585 68 HOH HOH . Q 8 HOH B 86 586 112 HOH HOH . Q 8 HOH B 87 587 145 HOH HOH . Q 8 HOH B 88 588 114 HOH HOH . Q 8 HOH B 89 589 61 HOH HOH . Q 8 HOH B 90 590 116 HOH HOH . Q 8 HOH B 91 591 166 HOH HOH . Q 8 HOH B 92 592 142 HOH HOH . Q 8 HOH B 93 593 190 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 MLA . . . K 4 -17.883 19.271 -11.999 1 37.83 ? C1 MLA 405 B 1 HETATM 2 O O1A MLA . . . K 4 -17.664 18.783 -10.833 1 31.63 ? O1A MLA 405 B 1 HETATM 3 O O1B MLA . . . K 4 -18.814 20.115 -12.209 1 29.68 ? O1B MLA 405 B 1 HETATM 4 C C2 MLA . . . K 4 -16.994 18.778 -13.169 1 38.81 ? C2 MLA 405 B 1 HETATM 5 C C3 MLA . . . K 4 -17.598 17.59 -13.92 1 41.12 ? C3 MLA 405 B 1 HETATM 6 O O3A MLA . . . K 4 -16.942 16.992 -14.804 1 44.15 ? O3A MLA 405 B 1 HETATM 7 O O3B MLA . . . K 4 -18.747 17.186 -13.669 1 39.92 ? O3B MLA 405 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 7 #