data_4WMB # _model_server_result.job_id 9PFRiVh09LueqaD5DkzhtA _model_server_result.datetime_utc '2024-12-26 19:18:30' _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 4wmb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 4WMB # _exptl.entry_id 4WMB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 54.938 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MANGANESE (II) ION' _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 4WMB _cell.length_a 89.468 _cell.length_b 89.468 _cell.length_c 42.934 _cell.Z_PDB 3 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4WMB _symmetry.cell_setting ? _symmetry.Int_Tables_number 143 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 3' # _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 _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _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 XYS _pdbx_entity_branch_link.comp_id_2 BGC _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 O3 _pdbx_entity_branch_link.leaving_atom_id_2 HO3 _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 3 n C BGC 1 B 1 BGC E 1 GCX 3 n C XYS 2 B 2 XYS E 1 GCX # 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 263 A CYS 349 1_555 A SG CYS 288 A CYS 374 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 A SG CYS 270 A CYS 356 1_555 A SG CYS 299 A CYS 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf3 B SG CYS 9 D CYS 51 1_555 B SG CYS 20 D CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf4 B SG CYS 14 D CYS 56 1_555 B SG CYS 29 D CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 B SG CYS 31 D CYS 73 1_555 B SG CYS 40 D CYS 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? covale ? covale1 B OG SER 11 D SER 53 1_555 C C1 BGC . B BGC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.618 sing covale ? covale2 C O3 BGC . B BGC 1 1_555 C C1 XYS . B XYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 sing metalc ? metalc1 A OD2 ASP 139 A ASP 225 1_555 D MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc2 A OD1 ASP 141 A ASP 227 1_555 D MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc3 A OD2 ASP 141 A ASP 227 1_555 D MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc4 A NE2 HIS 296 A HIS 382 1_555 D MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc5 D MN MN . A MN 401 1_555 E O1A UDP . A UDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc6 D MN MN . A MN 401 1_555 E O3B UDP . A UDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.903 ? # _chem_comp.formula 'Mn 2' _chem_comp.formula_weight 54.938 _chem_comp.id MN _chem_comp.mon_nstd_flag . _chem_comp.name 'MANGANESE (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 4WMB _atom_sites.fract_transf_matrix[1][1] 0.011177 _atom_sites.fract_transf_matrix[1][2] 0.006453 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012906 _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] 0.023292 _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 D 4 MN A 1 401 1 MN MN . E 5 UDP A 1 402 1 UDP UDP . F 6 SO4 A 1 403 1 SO4 SO4 . G 7 HOH A 1 501 52 HOH HOH . G 7 HOH A 2 502 57 HOH HOH . G 7 HOH A 3 503 12 HOH HOH . G 7 HOH A 4 504 8 HOH HOH . G 7 HOH A 5 505 62 HOH HOH . G 7 HOH A 6 506 1 HOH HOH . G 7 HOH A 7 507 61 HOH HOH . G 7 HOH A 8 508 7 HOH HOH . G 7 HOH A 9 509 36 HOH HOH . G 7 HOH A 10 510 58 HOH HOH . G 7 HOH A 11 511 3 HOH HOH . G 7 HOH A 12 512 4 HOH HOH . G 7 HOH A 13 513 5 HOH HOH . G 7 HOH A 14 514 6 HOH HOH . G 7 HOH A 15 515 9 HOH HOH . G 7 HOH A 16 516 11 HOH HOH . G 7 HOH A 17 517 13 HOH HOH . G 7 HOH A 18 518 14 HOH HOH . G 7 HOH A 19 519 15 HOH HOH . G 7 HOH A 20 520 16 HOH HOH . G 7 HOH A 21 521 17 HOH HOH . G 7 HOH A 22 522 18 HOH HOH . G 7 HOH A 23 523 19 HOH HOH . G 7 HOH A 24 524 20 HOH HOH . G 7 HOH A 25 525 21 HOH HOH . G 7 HOH A 26 526 23 HOH HOH . G 7 HOH A 27 527 24 HOH HOH . G 7 HOH A 28 528 25 HOH HOH . G 7 HOH A 29 529 26 HOH HOH . G 7 HOH A 30 530 27 HOH HOH . G 7 HOH A 31 531 29 HOH HOH . G 7 HOH A 32 532 30 HOH HOH . G 7 HOH A 33 533 31 HOH HOH . G 7 HOH A 34 534 32 HOH HOH . G 7 HOH A 35 535 34 HOH HOH . G 7 HOH A 36 536 35 HOH HOH . G 7 HOH A 37 537 37 HOH HOH . G 7 HOH A 38 538 38 HOH HOH . G 7 HOH A 39 539 39 HOH HOH . G 7 HOH A 40 540 40 HOH HOH . G 7 HOH A 41 541 41 HOH HOH . G 7 HOH A 42 542 42 HOH HOH . G 7 HOH A 43 543 43 HOH HOH . G 7 HOH A 44 544 44 HOH HOH . G 7 HOH A 45 545 45 HOH HOH . G 7 HOH A 46 546 46 HOH HOH . G 7 HOH A 47 547 48 HOH HOH . G 7 HOH A 48 548 49 HOH HOH . G 7 HOH A 49 549 50 HOH HOH . G 7 HOH A 50 550 51 HOH HOH . G 7 HOH A 51 551 53 HOH HOH . G 7 HOH A 52 552 54 HOH HOH . G 7 HOH A 53 553 55 HOH HOH . G 7 HOH A 54 554 56 HOH HOH . G 7 HOH A 55 555 59 HOH HOH . G 7 HOH A 56 556 60 HOH HOH . G 7 HOH A 57 557 63 HOH HOH . G 7 HOH A 58 558 64 HOH HOH . G 7 HOH A 59 559 65 HOH HOH . G 7 HOH A 60 560 67 HOH HOH . G 7 HOH A 61 561 68 HOH HOH . G 7 HOH A 62 562 69 HOH HOH . G 7 HOH A 63 563 70 HOH HOH . G 7 HOH A 64 564 71 HOH HOH . G 7 HOH A 65 565 72 HOH HOH . H 7 HOH D 1 201 2 HOH HOH . H 7 HOH D 2 202 10 HOH HOH . H 7 HOH D 3 203 22 HOH HOH . H 7 HOH D 4 204 28 HOH HOH . H 7 HOH D 5 205 33 HOH HOH . H 7 HOH D 6 206 66 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol MN _atom_site.label_atom_id MN _atom_site.label_comp_id MN _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id D _atom_site.label_entity_id 4 _atom_site.Cartn_x 28.04 _atom_site.Cartn_y 5.55 _atom_site.Cartn_z 8.545 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 27.01 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MN _atom_site.auth_comp_id MN _atom_site.auth_seq_id 401 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 23 _model_server_stats.element_count 1 #