data_8J4Y # _model_server_result.job_id XpnquXtCRhFnloDFr2LVOQ _model_server_result.datetime_utc '2024-10-16 14:12:54' _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 8j4y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":402}' # _entry.id 8J4Y # _exptl.entry_id 8J4Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 54.938 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MANGANESE (II) ION' _entity.pdbx_number_of_molecules 12 _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 8J4Y _cell.length_a 160.43 _cell.length_b 160.43 _cell.length_c 310.4 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8J4Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall 'P 4n 2n' _symmetry.space_group_name_H-M 'P 42 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA trimeric 3 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,G,I,J,K,O,P,Q,BA,EA 1 1 B,L,M,N,DA 2 1,2 D,F,H,R,S,T,U,X,Y,Z,AA,CA,FA,HA,IA 3 1 E,V,W,GA 4 1,3 # 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_445 -x-1,-y-1,z -1 0 0 0 -1 0 0 0 1 -160.43 -160.43 0 3 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 I N N ? 3 J N N ? 3 L N N ? 3 M N N ? 3 O N N ? 3 P N N ? 3 R N N ? 3 S N N ? 3 V N N ? 3 W N N ? 3 X N N ? 3 Y 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 OD1 ASP 72 A ASP 72 1_555 J MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc2 A OE2 GLU 103 A GLU 103 1_555 I MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc3 A OE1 GLU 103 A GLU 103 1_555 J MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc4 A ND1 HIS 106 A HIS 106 1_555 J MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc5 A OE1 GLU 163 A GLU 163 1_555 I MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc6 A OE1 GLU 197 A GLU 197 1_555 I MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? metalc ? metalc7 A OE2 GLU 197 A GLU 197 1_555 J MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc8 A ND1 HIS 200 A HIS 200 1_555 I MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc9 B OD1 ASP 72 B ASP 72 1_555 M MN MN . B MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.564 ? metalc ? metalc10 B OE2 GLU 103 B GLU 103 1_555 L MN MN . B MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc11 B ND1 HIS 106 B HIS 106 1_555 M MN MN . B MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc12 B OE2 GLU 163 B GLU 163 1_555 L MN MN . B MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? metalc ? metalc13 B OE1 GLU 197 B GLU 197 1_555 L MN MN . B MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.606 ? metalc ? metalc14 B OE2 GLU 197 B GLU 197 1_555 M MN MN . B MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc15 B ND1 HIS 200 B HIS 200 1_555 L MN MN . B MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc16 C OD1 ASP 72 C ASP 72 1_555 P MN MN . C MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc17 C OE2 GLU 103 C GLU 103 1_555 O MN MN . C MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc18 C OE1 GLU 103 C GLU 103 1_555 P MN MN . C MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? metalc ? metalc19 C ND1 HIS 106 C HIS 106 1_555 P MN MN . C MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? metalc ? metalc20 C OE1 GLU 163 C GLU 163 1_555 O MN MN . C MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? metalc ? metalc21 C OE1 GLU 197 C GLU 197 1_555 O MN MN . C MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? metalc ? metalc22 C OE2 GLU 197 C GLU 197 1_555 O MN MN . C MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? metalc ? metalc23 C OE2 GLU 197 C GLU 197 1_555 P MN MN . C MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc24 C ND1 HIS 200 C HIS 200 1_555 O MN MN . C MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc25 D OD1 ASP 72 D ASP 72 1_555 S MN MN . D MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc26 D OE2 GLU 103 D GLU 103 1_555 R MN MN . D MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc27 D OE2 GLU 103 D GLU 103 1_555 S MN MN . D MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.52 ? metalc ? metalc28 D ND1 HIS 106 D HIS 106 1_555 S MN MN . D MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc29 D OE1 GLU 163 D GLU 163 1_555 R MN MN . D MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc30 D OE2 GLU 197 D GLU 197 1_555 R MN MN . D MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc31 D OE2 GLU 197 D GLU 197 1_555 S MN MN . D MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc32 D ND1 HIS 200 D HIS 200 1_555 R MN MN . D MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc33 E OD1 ASP 72 E ASP 72 1_555 W MN MN . E MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc34 E OE2 GLU 103 E GLU 103 1_555 V MN MN . E MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc35 E OE1 GLU 197 E GLU 197 1_555 V MN MN . E MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.573 ? metalc ? metalc36 E OE2 GLU 197 E GLU 197 1_555 W MN MN . E MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.567 ? metalc ? metalc37 E ND1 HIS 200 E HIS 200 1_555 V MN MN . E MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc38 F OD1 ASP 72 F ASP 72 1_555 Y MN MN . F MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc39 F OE2 GLU 103 F GLU 103 1_555 X MN MN . F MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc40 F ND1 HIS 106 F HIS 106 1_555 Y MN MN . F MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc41 F OE1 GLU 163 F GLU 163 1_555 X MN MN . F MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc42 F OE2 GLU 163 F GLU 163 1_555 X MN MN . F MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? metalc ? metalc43 F OE1 GLU 197 F GLU 197 1_555 X MN MN . F MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.797 ? metalc ? metalc44 F OE2 GLU 197 F GLU 197 1_555 Y MN MN . F MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc45 F ND1 HIS 200 F HIS 200 1_555 X MN MN . F MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? # _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 8J4Y _atom_sites.fract_transf_matrix[1][1] 0.006233 _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] 0.006233 _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] 0.003222 _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 I 3 MN A 1 401 301 MN MN . J 3 MN A 1 402 302 MN MN . K 4 PER A 1 403 303 PER PER . L 3 MN B 1 401 301 MN MN . M 3 MN B 1 402 302 MN MN . N 5 OH B 1 403 303 OH OH . O 3 MN C 1 401 301 MN MN . P 3 MN C 1 402 302 MN MN . Q 5 OH C 1 403 303 OH OH . R 3 MN D 1 401 301 MN MN . S 3 MN D 1 402 302 MN MN . T 4 PER D 1 403 303 PER PER . U 5 OH D 1 404 304 OH OH . V 3 MN E 1 401 301 MN MN . W 3 MN E 1 402 302 MN MN . X 3 MN F 1 401 301 MN MN . Y 3 MN F 1 402 302 MN MN . Z 4 PER F 1 403 303 PER PER . AA 5 OH F 1 404 304 OH OH . BA 6 FMN G 1 201 153 FMN FMN . CA 6 FMN I 1 201 152 FMN FMN . DA 7 HOH B 1 501 14 HOH HOH . DA 7 HOH B 2 502 12 HOH HOH . DA 7 HOH B 3 503 28 HOH HOH . DA 7 HOH B 4 504 15 HOH HOH . EA 7 HOH C 1 501 29 HOH HOH . EA 7 HOH C 2 502 18 HOH HOH . FA 7 HOH D 1 501 22 HOH HOH . FA 7 HOH D 2 502 20 HOH HOH . FA 7 HOH D 3 503 19 HOH HOH . FA 7 HOH D 4 504 2 HOH HOH . GA 7 HOH E 1 501 4 HOH HOH . GA 7 HOH E 2 502 24 HOH HOH . HA 7 HOH F 1 501 25 HOH HOH . HA 7 HOH F 2 502 27 HOH HOH . HA 7 HOH F 3 503 5 HOH HOH . IA 7 HOH I 1 301 1 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 Y _atom_site.label_entity_id 3 _atom_site.Cartn_x -20.802 _atom_site.Cartn_y -66.054 _atom_site.Cartn_z -77.626 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 70.48 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MN _atom_site.auth_comp_id MN _atom_site.auth_seq_id 402 _atom_site.auth_asym_id F _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #