data_3LCB # _model_server_result.job_id L9Xrh6ZhaZp28LOCZ_JdvA _model_server_result.datetime_utc '2024-11-09 02:40:09' _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 3lcb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1604}' # _entry.id 3LCB # _exptl.entry_id 3LCB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ADENOSINE MONOPHOSPHATE' _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 120 _cell.entry_id 3LCB _cell.length_a 196.801 _cell.length_b 196.801 _cell.length_c 156.458 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LCB _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dodecameric 12 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,E,F,G,K 1 1 D,N 1 2 B,C,H,I,J,L,M 2 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N 3 1,3,2 # 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_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 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 E N N ? 3 I 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 ASN 462 A ASN 462 1_555 G MG MG . A MG 579 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc2 A OD2 ASP 475 A ASP 475 1_555 G MG MG . A MG 579 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? metalc ? metalc3 A OD1 ASP 475 A ASP 475 1_555 G MG MG . A MG 579 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.794 ? metalc ? metalc4 G MG MG . A MG 579 1_555 F O1A ATP . A ATP 1760 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc5 G MG MG . A MG 579 1_555 F O1G ATP . A ATP 1760 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc6 G MG MG . A MG 579 1_555 F O1B ATP . A ATP 1760 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? metalc ? metalc7 G MG MG . A MG 579 1_555 F O3B ATP . A ATP 1760 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.786 ? metalc ? metalc8 B OD1 ASN 462 B ASN 462 1_555 J MG MG . B MG 579 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc9 J MG MG . B MG 579 1_555 H O1B ATP . B ATP 1761 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.88 ? metalc ? metalc10 J MG MG . B MG 579 1_555 H O3A ATP . B ATP 1761 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc11 J MG MG . B MG 579 1_555 H O2B ATP . B ATP 1761 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.866 ? metalc ? metalc12 J MG MG . B MG 579 1_555 H O5' ATP . B ATP 1761 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.939 ? metalc ? metalc13 J MG MG . B MG 579 1_555 H O2A ATP . B ATP 1761 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.944 ? # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id AMP _chem_comp.mon_nstd_flag . _chem_comp.name 'ADENOSINE MONOPHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag P O1P AMP doub 13 n n P O2P AMP sing 14 n n P O3P AMP sing 15 n n P O5' AMP sing 16 n n O2P HOP2 AMP sing 17 n n O3P HOP3 AMP sing 18 n n O5' C5' AMP sing 19 n n C5' C4' AMP sing 20 n n C5' "H5'1" AMP sing 21 n n C5' "H5'2" AMP sing 22 n n C4' O4' AMP sing 23 n n C4' C3' AMP sing 24 n n C4' H4' AMP sing 25 n n O4' C1' AMP sing 26 n n C3' O3' AMP sing 27 n n C3' C2' AMP sing 28 n n C3' H3' AMP sing 29 n n O3' HO3' AMP sing 30 n n C2' O2' AMP sing 31 n n C2' C1' AMP sing 32 n n C2' H2' AMP sing 33 n n O2' HO2' AMP sing 34 n n C1' N9 AMP sing 35 n n C1' H1' AMP sing 36 n n N9 C8 AMP sing 37 n y N9 C4 AMP sing 38 n y C8 N7 AMP doub 39 n y C8 H8 AMP sing 40 n n N7 C5 AMP sing 41 n y C5 C6 AMP sing 42 n y C5 C4 AMP doub 43 n y C6 N6 AMP sing 44 n n C6 N1 AMP doub 45 n y N6 HN61 AMP sing 46 n n N6 HN62 AMP sing 47 n n N1 C2 AMP sing 48 n y C2 N3 AMP doub 49 n y C2 H2 AMP sing 50 n n N3 C4 AMP sing 51 n y # _atom_sites.entry_id 3LCB _atom_sites.fract_transf_matrix[1][1] 0.005081 _atom_sites.fract_transf_matrix[1][2] 0.002934 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005867 _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] 0.006391 _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 E 3 AMP A 1 1604 1604 AMP AMP . F 4 ATP A 1 1760 1760 ATP ATP . G 5 MG A 1 579 1 MG MG . H 4 ATP B 1 1761 1761 ATP ATP . I 3 AMP B 1 1604 1604 AMP AMP . J 5 MG B 1 579 1 MG MG . K 6 HOH A 1 580 8 HOH HOH . K 6 HOH A 2 581 15 HOH HOH . K 6 HOH A 3 582 20 HOH HOH . L 6 HOH B 1 580 7 HOH HOH . L 6 HOH B 2 581 9 HOH HOH . L 6 HOH B 3 582 13 HOH HOH . L 6 HOH B 4 583 19 HOH HOH . L 6 HOH B 5 584 21 HOH HOH . M 6 HOH C 1 417 1 HOH HOH . M 6 HOH C 2 418 3 HOH HOH . M 6 HOH C 3 419 6 HOH HOH . M 6 HOH C 4 420 12 HOH HOH . M 6 HOH C 5 421 14 HOH HOH . N 6 HOH D 1 417 2 HOH HOH . N 6 HOH D 2 418 4 HOH HOH . N 6 HOH D 3 419 5 HOH HOH . N 6 HOH D 4 420 10 HOH HOH . N 6 HOH D 5 421 11 HOH HOH . N 6 HOH D 6 422 16 HOH HOH . N 6 HOH D 7 423 17 HOH HOH . N 6 HOH D 8 424 18 HOH HOH . # 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 P AMP . . . E 3 -36.728 35.081 -49.211 1 65.41 ? P AMP 1604 A 1 HETATM 2 O O1P AMP . . . E 3 -37.462 34.385 -48.088 1 65.54 ? O1P AMP 1604 A 1 HETATM 3 O O2P AMP . . . E 3 -35.33 34.553 -49.423 1 64.95 ? O2P AMP 1604 A 1 HETATM 4 O O3P AMP . . . E 3 -36.833 36.59 -49.182 1 64.88 ? O3P AMP 1604 A 1 HETATM 5 O O5' AMP . . . E 3 -37.521 34.661 -50.548 1 65.21 ? O5' AMP 1604 A 1 HETATM 6 C C5' AMP . . . E 3 -38.92 34.906 -50.708 1 65.71 ? C5' AMP 1604 A 1 HETATM 7 C C4' AMP . . . E 3 -39.34 34.536 -52.127 1 66.65 ? C4' AMP 1604 A 1 HETATM 8 O O4' AMP . . . E 3 -38.564 35.278 -53.075 1 66.94 ? O4' AMP 1604 A 1 HETATM 9 C C3' AMP . . . E 3 -39.104 33.059 -52.422 1 66.78 ? C3' AMP 1604 A 1 HETATM 10 O O3' AMP . . . E 3 -40.256 32.486 -53.051 1 66.29 ? O3' AMP 1604 A 1 HETATM 11 C C2' AMP . . . E 3 -37.92 33.02 -53.367 1 66.68 ? C2' AMP 1604 A 1 HETATM 12 O O2' AMP . . . E 3 -38.088 32.01 -54.359 1 66.87 ? O2' AMP 1604 A 1 HETATM 13 C C1' AMP . . . E 3 -37.912 34.4 -53.995 1 66.96 ? C1' AMP 1604 A 1 HETATM 14 N N9 AMP . . . E 3 -36.529 34.862 -54.238 1 67.23 ? N9 AMP 1604 A 1 HETATM 15 C C8 AMP . . . E 3 -35.619 35.22 -53.311 1 67.43 ? C8 AMP 1604 A 1 HETATM 16 N N7 AMP . . . E 3 -34.451 35.602 -53.887 1 67.54 ? N7 AMP 1604 A 1 HETATM 17 C C5 AMP . . . E 3 -34.616 35.496 -55.219 1 67.61 ? C5 AMP 1604 A 1 HETATM 18 C C6 AMP . . . E 3 -33.786 35.734 -56.422 1 67.82 ? C6 AMP 1604 A 1 HETATM 19 N N6 AMP . . . E 3 -32.512 36.174 -56.304 1 67.89 ? N6 AMP 1604 A 1 HETATM 20 N N1 AMP . . . E 3 -34.341 35.49 -57.634 1 68.17 ? N1 AMP 1604 A 1 HETATM 21 C C2 AMP . . . E 3 -35.607 35.042 -57.761 1 67.92 ? C2 AMP 1604 A 1 HETATM 22 N N3 AMP . . . E 3 -36.42 34.804 -56.718 1 67.69 ? N3 AMP 1604 A 1 HETATM 23 C C4 AMP . . . E 3 -35.986 35.006 -55.445 1 67.57 ? C4 AMP 1604 A 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 23 #