data_4KQB # _model_server_result.job_id '_Ptl7sPnVmFLc5aukaZaCA' _model_server_result.datetime_utc '2024-11-15 21:54:55' _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":"M","auth_seq_id":608}' # _entry.id 4KQB # _exptl.entry_id 4KQB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 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 ? 5 I N N ? 5 M 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 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 . # 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 P PB ADP . . . M 5 55.612 30.509 187.268 1 60.83 ? PB ADP 608 B 1 HETATM 2 O O1B ADP . . . M 5 56.684 29.849 186.435 1 58.53 ? O1B ADP 608 B 1 HETATM 3 O O2B ADP . . . M 5 56.023 31.829 187.874 1 63.48 ? O2B ADP 608 B 1 HETATM 4 O O3B ADP . . . M 5 54.238 30.519 186.646 1 60.72 ? O3B ADP 608 B 1 HETATM 5 P PA ADP . . . M 5 55.017 27.987 188.351 1 50.83 ? PA ADP 608 B 1 HETATM 6 O O1A ADP . . . M 5 56.091 27.309 187.535 1 53.43 ? O1A ADP 608 B 1 HETATM 7 O O2A ADP . . . M 5 53.569 27.917 187.93 1 47.41 ? O2A ADP 608 B 1 HETATM 8 O O3A ADP . . . M 5 55.438 29.532 188.534 1 165.01 ? O3A ADP 608 B 1 HETATM 9 O O5' ADP . . . M 5 55.142 27.462 189.864 1 68.78 ? O5' ADP 608 B 1 HETATM 10 C C5' ADP . . . M 5 56.324 27.774 190.597 1 70.14 ? C5' ADP 608 B 1 HETATM 11 C C4' ADP . . . M 5 56.713 26.6 191.479 1 71.95 ? C4' ADP 608 B 1 HETATM 12 O O4' ADP . . . M 5 55.59 26.186 192.256 1 70.52 ? O4' ADP 608 B 1 HETATM 13 C C3' ADP . . . M 5 57.142 25.411 190.638 1 74.99 ? C3' ADP 608 B 1 HETATM 14 O O3' ADP . . . M 5 58.568 25.297 190.617 1 77.54 ? O3' ADP 608 B 1 HETATM 15 C C2' ADP . . . M 5 56.517 24.208 191.311 1 73.63 ? C2' ADP 608 B 1 HETATM 16 O O2' ADP . . . M 5 57.523 23.514 192.053 1 74.62 ? O2' ADP 608 B 1 HETATM 17 C C1' ADP . . . M 5 55.468 24.764 192.261 1 71.08 ? C1' ADP 608 B 1 HETATM 18 N N9 ADP . . . M 5 54.127 24.391 191.751 1 70.73 ? N9 ADP 608 B 1 HETATM 19 C C8 ADP . . . M 5 53.622 24.762 190.559 1 71.83 ? C8 ADP 608 B 1 HETATM 20 N N7 ADP . . . M 5 52.375 24.258 190.375 1 71.76 ? N7 ADP 608 B 1 HETATM 21 C C5 ADP . . . M 5 52.066 23.542 191.47 1 70.81 ? C5 ADP 608 B 1 HETATM 22 C C6 ADP . . . M 5 50.904 22.745 191.928 1 68.94 ? C6 ADP 608 B 1 HETATM 23 N N6 ADP . . . M 5 49.797 22.615 191.155 1 67.4 ? N6 ADP 608 B 1 HETATM 24 N N1 ADP . . . M 5 50.985 22.157 193.142 1 67.96 ? N1 ADP 608 B 1 HETATM 25 C C2 ADP . . . M 5 52.079 22.282 193.917 1 67.34 ? C2 ADP 608 B 1 HETATM 26 N N3 ADP . . . M 5 53.169 22.987 193.565 1 68.22 ? N3 ADP 608 B 1 HETATM 27 C C4 ADP . . . M 5 53.225 23.628 192.374 1 70.07 ? C4 ADP 608 B 1 # _model_server_stats.io_time_ms 115 _model_server_stats.parse_time_ms 78 _model_server_stats.create_model_time_ms 130 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #