data_4KQB # _model_server_result.job_id GyxUIZHcGK1sF6C327BMcg _model_server_result.datetime_utc '2024-11-15 21:29:00' _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 4kqb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":606}' # _entry.id 4KQB # _exptl.entry_id 4KQB _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 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 4KQB _cell.length_a 58.49 _cell.length_b 101.702 _cell.length_c 158.765 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KQB _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G,H,I,J 1 1 B,E,F,K,L,M 2 1 A,C,D,G,H,I,J 3 1 B,E,F,K,L,M 3 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' 3_747 -x+2,y-1/2,-z+5/2 -1 0 0 0 1 0 0 0 -1 116.98 -50.851 396.9125 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 G N N ? 4 H N N ? 4 K N N ? 4 L N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 MAN NAG C1 O1 . O4 HO4 . sing 3 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . 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 A 601 NAG 2 n C NAG 2 C 2 NAG A 602 NAG 2 n C MAN 3 C 3 MAN A 603 BMA 3 n D NAG 1 D 1 NAG A 604 NAG 3 n D NAG 2 D 2 NAG A 605 NAG 2 n E NAG 1 E 1 NAG B 601 NAG 2 n E NAG 2 E 2 NAG B 602 NAG 2 n E MAN 3 E 3 MAN B 603 BMA 3 n F NAG 1 F 1 NAG B 604 NAG 3 n F NAG 2 F 2 NAG B 605 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 51 A CYS 110 1_555 A SG CYS 85 A CYS 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 209 A CYS 268 1_555 A SG CYS 225 A CYS 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 214 A CYS 273 1_555 A SG CYS 218 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 A SG CYS 274 A CYS 333 1_555 A SG CYS 350 A CYS 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 A SG CYS 351 A CYS 410 1_555 A SG CYS 410 A CYS 469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 B SG CYS 51 B CYS 110 1_555 B SG CYS 85 B CYS 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 B SG CYS 209 B CYS 268 1_555 B SG CYS 225 B CYS 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 B SG CYS 214 B CYS 273 1_555 B SG CYS 218 B CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf9 B SG CYS 274 B CYS 333 1_555 B SG CYS 350 B CYS 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf10 B SG CYS 351 B CYS 410 1_555 B SG CYS 410 B CYS 469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A ND2 ASN 54 A ASN 113 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.395 ? covale ? covale2 A ND2 ASN 183 A ASN 242 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.487 ? covale ? covale3 B ND2 ASN 54 B ASN 113 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale4 B ND2 ASN 183 B ASN 242 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.41 ? covale ? covale6 C O4 NAG . C NAG 2 1_555 C C1 MAN . C MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.406 ? covale ? covale7 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale8 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.418 ? covale ? covale9 E O4 NAG . E NAG 2 1_555 E C1 MAN . E MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.416 ? covale ? covale10 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? metalc ? metalc1 A OE1 GLU 154 A GLU 213 1_555 G MN MN . A MN 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc2 A NE2 HIS 222 A HIS 281 1_555 J NI NI . A NI 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc3 A OD1 ASP 328 A ASP 387 1_555 G MN MN . A MN 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc4 A OD2 ASP 328 A ASP 387 1_555 H MN MN . A MN 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc5 G MN MN . A MN 606 1_555 I O3B ADP . A ADP 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc6 H MN MN . A MN 607 1_555 I O3B ADP . A ADP 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.13 ? metalc ? metalc7 H MN MN . A MN 607 1_555 I O1A ADP . A ADP 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc8 H MN MN . A MN 607 1_555 I O1B ADP . A ADP 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.707 ? metalc ? metalc9 B OE1 GLU 154 B GLU 213 1_555 K MN MN . B MN 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc10 B OD1 ASP 328 B ASP 387 1_555 K MN MN . B MN 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.518 ? metalc ? metalc11 B OD2 ASP 328 B ASP 387 1_555 L MN MN . B MN 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc12 L MN MN . B MN 607 1_555 M O1B ADP . B ADP 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc13 L MN MN . B MN 607 1_555 M O1A ADP . B ADP 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? # _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 4KQB _atom_sites.fract_transf_matrix[1][1] 0.017097 _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] 0.009833 _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] 0.006299 _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 G 4 MN A 1 606 701 MN MN . H 4 MN A 1 607 702 MN MN . I 5 ADP A 1 608 800 ADP ADP . J 6 NI A 1 609 1 NI NI . K 4 MN B 1 606 701 MN MN . L 4 MN B 1 607 702 MN MN . M 5 ADP B 1 608 800 ADP ADP . # _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 K _atom_site.label_entity_id 4 _atom_site.Cartn_x 55.835 _atom_site.Cartn_y 30.361 _atom_site.Cartn_z 183.521 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 76.56 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MN _atom_site.auth_comp_id MN _atom_site.auth_seq_id 606 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 73 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 1 #