data_4YVZ # _model_server_result.job_id ZKwnRni7Vhx4owTryIfR6w _model_server_result.datetime_utc '2024-11-19 08:24:00' _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 4yvz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":403}' # _entry.id 4YVZ # _exptl.entry_id 4YVZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 54.938 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MANGANESE (II) ION' _entity.pdbx_number_of_molecules 4 _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 4YVZ _cell.length_a 107.49 _cell.length_b 107.49 _cell.length_c 168.79 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YVZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 90 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 4 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details Octameric _pdbx_struct_assembly.oligomeric_count 8 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 2_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 0 -107.49 0 3 'crystal symmetry operation' 3_445 -y-1/2,x-1/2,z 0 -1 0 1 0 0 0 0 1 -53.745 -53.745 0 4 'crystal symmetry operation' 4_545 y+1/2,-x-1/2,z 0 1 0 -1 0 0 0 0 1 53.745 -53.745 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N ? 2 G N N ? 2 H N 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 95 A ASP 75 1_555 C MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc2 A O GLU 249 A GLU 229 1_555 D MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc3 A OD1 ASP 252 A ASP 232 1_555 D MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc4 C MN MN . A MN 401 1_555 E O3G 3AT . A 3AT 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc5 C MN MN . A MN 401 1_555 E O2B 3AT . A 3AT 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc6 C MN MN . A MN 401 1_555 E O1A 3AT . A 3AT 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc7 C MN MN . A MN 401 1_555 I O HOH . A HOH 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc8 C MN MN . A MN 401 1_555 J O HOH . B HOH 557 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc9 B OD2 ASP 95 B ASP 75 1_555 G MN MN . B MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc10 B O GLU 249 B GLU 229 1_555 H MN MN . B MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc11 B OD1 ASP 252 B ASP 232 1_555 H MN MN . B MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? metalc ? metalc12 B OD2 ASP 252 B ASP 232 1_555 H MN MN . B MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.682 ? metalc ? metalc13 B OD1 ASP 253 B ASP 233 1_555 H MN MN . B MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? metalc ? metalc14 F O1G 3AT . B 3AT 401 1_555 G MN MN . B MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc15 F O1B 3AT . B 3AT 401 1_555 G MN MN . B MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc16 F O2A 3AT . B 3AT 401 1_555 G MN MN . B MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc17 G MN MN . B MN 402 1_555 J O HOH . B HOH 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc18 G MN MN . B MN 402 1_555 J O HOH . B HOH 549 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? # _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 4YVZ _atom_sites.fract_transf_matrix[1][1] 0.009303 _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] 0.009303 _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] 0.005925 _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 C 2 MN A 1 401 1 MN MN . D 2 MN A 1 402 3 MN MN . E 3 3AT A 1 403 1 3AT 3AT . F 3 3AT B 1 401 2 3AT 3AT . G 2 MN B 1 402 2 MN MN . H 2 MN B 1 403 4 MN MN . I 4 HOH A 1 501 7 HOH HOH . I 4 HOH A 2 502 45 HOH HOH . I 4 HOH A 3 503 28 HOH HOH . I 4 HOH A 4 504 51 HOH HOH . I 4 HOH A 5 505 5 HOH HOH . I 4 HOH A 6 506 105 HOH HOH . I 4 HOH A 7 507 85 HOH HOH . I 4 HOH A 8 508 89 HOH HOH . I 4 HOH A 9 509 88 HOH HOH . I 4 HOH A 10 510 2 HOH HOH . I 4 HOH A 11 511 102 HOH HOH . I 4 HOH A 12 512 10 HOH HOH . I 4 HOH A 13 513 4 HOH HOH . I 4 HOH A 14 514 69 HOH HOH . I 4 HOH A 15 515 71 HOH HOH . I 4 HOH A 16 516 74 HOH HOH . I 4 HOH A 17 517 8 HOH HOH . I 4 HOH A 18 518 1 HOH HOH . I 4 HOH A 19 519 37 HOH HOH . I 4 HOH A 20 520 107 HOH HOH . I 4 HOH A 21 521 17 HOH HOH . I 4 HOH A 22 522 92 HOH HOH . I 4 HOH A 23 523 56 HOH HOH . I 4 HOH A 24 524 108 HOH HOH . I 4 HOH A 25 525 6 HOH HOH . I 4 HOH A 26 526 42 HOH HOH . I 4 HOH A 27 527 76 HOH HOH . I 4 HOH A 28 528 49 HOH HOH . I 4 HOH A 29 529 82 HOH HOH . I 4 HOH A 30 530 109 HOH HOH . I 4 HOH A 31 531 41 HOH HOH . I 4 HOH A 32 532 98 HOH HOH . I 4 HOH A 33 533 66 HOH HOH . I 4 HOH A 34 534 9 HOH HOH . I 4 HOH A 35 535 93 HOH HOH . I 4 HOH A 36 536 44 HOH HOH . I 4 HOH A 37 537 20 HOH HOH . I 4 HOH A 38 538 81 HOH HOH . I 4 HOH A 39 539 3 HOH HOH . I 4 HOH A 40 540 53 HOH HOH . I 4 HOH A 41 541 30 HOH HOH . I 4 HOH A 42 542 87 HOH HOH . I 4 HOH A 43 543 19 HOH HOH . I 4 HOH A 44 544 83 HOH HOH . I 4 HOH A 45 545 110 HOH HOH . I 4 HOH A 46 546 18 HOH HOH . I 4 HOH A 47 547 72 HOH HOH . I 4 HOH A 48 548 111 HOH HOH . I 4 HOH A 49 549 38 HOH HOH . J 4 HOH B 1 501 84 HOH HOH . J 4 HOH B 2 502 47 HOH HOH . J 4 HOH B 3 503 55 HOH HOH . J 4 HOH B 4 504 22 HOH HOH . J 4 HOH B 5 505 11 HOH HOH . J 4 HOH B 6 506 14 HOH HOH . J 4 HOH B 7 507 86 HOH HOH . J 4 HOH B 8 508 94 HOH HOH . J 4 HOH B 9 509 78 HOH HOH . J 4 HOH B 10 510 13 HOH HOH . J 4 HOH B 11 511 12 HOH HOH . J 4 HOH B 12 512 59 HOH HOH . J 4 HOH B 13 513 36 HOH HOH . J 4 HOH B 14 514 95 HOH HOH . J 4 HOH B 15 515 39 HOH HOH . J 4 HOH B 16 516 70 HOH HOH . J 4 HOH B 17 517 29 HOH HOH . J 4 HOH B 18 518 62 HOH HOH . J 4 HOH B 19 519 33 HOH HOH . J 4 HOH B 20 520 24 HOH HOH . J 4 HOH B 21 521 46 HOH HOH . J 4 HOH B 22 522 48 HOH HOH . J 4 HOH B 23 523 61 HOH HOH . J 4 HOH B 24 524 68 HOH HOH . J 4 HOH B 25 525 43 HOH HOH . J 4 HOH B 26 526 23 HOH HOH . J 4 HOH B 27 527 79 HOH HOH . J 4 HOH B 28 528 103 HOH HOH . J 4 HOH B 29 529 75 HOH HOH . J 4 HOH B 30 530 25 HOH HOH . J 4 HOH B 31 531 96 HOH HOH . J 4 HOH B 32 532 58 HOH HOH . J 4 HOH B 33 533 64 HOH HOH . J 4 HOH B 34 534 15 HOH HOH . J 4 HOH B 35 535 40 HOH HOH . J 4 HOH B 36 536 54 HOH HOH . J 4 HOH B 37 537 77 HOH HOH . J 4 HOH B 38 538 60 HOH HOH . J 4 HOH B 39 539 106 HOH HOH . J 4 HOH B 40 540 34 HOH HOH . J 4 HOH B 41 541 100 HOH HOH . J 4 HOH B 42 542 97 HOH HOH . J 4 HOH B 43 543 101 HOH HOH . J 4 HOH B 44 544 67 HOH HOH . J 4 HOH B 45 545 91 HOH HOH . J 4 HOH B 46 546 73 HOH HOH . J 4 HOH B 47 547 35 HOH HOH . J 4 HOH B 48 548 32 HOH HOH . J 4 HOH B 49 549 26 HOH HOH . J 4 HOH B 50 550 16 HOH HOH . J 4 HOH B 51 551 31 HOH HOH . J 4 HOH B 52 552 50 HOH HOH . J 4 HOH B 53 553 52 HOH HOH . J 4 HOH B 54 554 57 HOH HOH . J 4 HOH B 55 555 80 HOH HOH . J 4 HOH B 56 556 99 HOH HOH . J 4 HOH B 57 557 27 HOH HOH . J 4 HOH B 58 558 90 HOH HOH . J 4 HOH B 59 559 21 HOH HOH . J 4 HOH B 60 560 63 HOH HOH . J 4 HOH B 61 561 104 HOH HOH . J 4 HOH B 62 562 65 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 H _atom_site.label_entity_id 2 _atom_site.Cartn_x 18.808 _atom_site.Cartn_y -41.788 _atom_site.Cartn_z -8.091 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 89.96 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MN _atom_site.auth_comp_id MN _atom_site.auth_seq_id 403 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 1 #