data_6GCN # _model_server_result.job_id kA0Zl8kgDAK6g_PDgCUpKA _model_server_result.datetime_utc '2024-10-28 02:25:34' _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 6gcn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":701}' # _entry.id 6GCN # _exptl.entry_id 6GCN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 120 _cell.entry_id 6GCN _cell.length_a 197.55 _cell.length_b 197.55 _cell.length_c 323.92 _cell.Z_PDB 72 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6GCN _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 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 hexameric 6 author_and_software_defined_assembly 1 PISA hexameric 6 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,I,J,O 1 1,2,3 C,D,K,L,M,N,P,Q 2 1,2,3 # 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_675 -y+1,x-y+2,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 342.166637 0 3 'crystal symmetry operation' 3_465 -x+y-1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -296.325 171.083319 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 G N N ? 2 K N N ? 2 M 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 disulf ? disulf1 A SG CYS 459 A CYS 588 1_555 A SG CYS 477 A CYS 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 B SG CYS 459 B CYS 588 1_555 B SG CYS 477 B CYS 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 C SG CYS 459 C CYS 588 1_555 C SG CYS 477 C CYS 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf4 D SG CYS 459 D CYS 588 1_555 D SG CYS 477 D CYS 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc1 A NE2 HIS 289 A HIS 418 1_555 F ZN ZN . A ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc2 A NH1 ARG 314 A ARG 443 1_555 F ZN ZN . A ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc3 A OD1 ASP 367 A ASP 496 1_555 F ZN ZN . A ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc4 A OD2 ASP 367 A ASP 496 1_555 F ZN ZN . A ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc5 F ZN ZN . A ZN 702 1_555 O O HOH . A HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc6 B NE2 HIS 289 B HIS 418 1_555 H ZN ZN . B ZN 702 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc7 B NE2 HIS 289 B HIS 418 1_555 H ZN ZN . B ZN 702 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc8 B NE2 HIS 293 B HIS 422 1_555 H ZN ZN . B ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc9 B OD1 ASP 367 B ASP 496 1_555 H ZN ZN . B ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc10 B OD2 ASP 367 B ASP 496 1_555 H ZN ZN . B ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc11 H ZN ZN . B ZN 702 1_555 J O ALA . B ALA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc12 H ZN ZN . B ZN 702 1_555 J OXT ALA . B ALA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc13 C NE2 HIS 289 C HIS 418 1_555 L ZN ZN . C ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc14 C OD1 ASP 367 C ASP 496 1_555 L ZN ZN . C ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc15 C OD2 ASP 367 C ASP 496 1_555 L ZN ZN . C ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc16 L ZN ZN . C ZN 702 1_555 P O HOH . C HOH 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc17 D NE2 HIS 289 D HIS 418 1_555 N ZN ZN . D ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc18 D NE2 HIS 293 D HIS 422 1_555 N ZN ZN . D ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc19 D OD1 ASP 367 D ASP 496 1_555 N ZN ZN . D ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc20 D OD2 ASP 367 D ASP 496 1_555 N ZN ZN . D ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc21 N ZN ZN . D ZN 702 1_555 Q O HOH . D HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? # _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 ? # 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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 6GCN _atom_sites.fract_transf_matrix[1][1] 0.005062 _atom_sites.fract_transf_matrix[1][2] 0.002923 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005845 _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] 0.003087 _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 2 ADP A 1 701 701 ADP ADP . F 3 ZN A 1 702 702 ZN ZN . G 2 ADP B 1 701 701 ADP ADP . H 3 ZN B 1 702 702 ZN ZN . I 4 ALA B 1 703 704 ALA ALA . J 4 ALA B 1 704 705 ALA ALA . K 2 ADP C 1 701 701 ADP ADP . L 3 ZN C 1 702 702 ZN ZN . M 2 ADP D 1 701 701 ADP ADP . N 3 ZN D 1 702 702 ZN ZN . O 5 HOH A 1 801 703 HOH HOH . P 5 HOH C 1 801 704 HOH HOH . P 5 HOH C 2 802 703 HOH HOH . Q 5 HOH D 1 801 703 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 PB ADP . . . E 2 -71.413 152.09 43.154 1 84.92 ? PB ADP 701 A 1 HETATM 2 O O1B ADP . . . E 2 -71.049 152.205 41.693 1 83.17 ? O1B ADP 701 A 1 HETATM 3 O O2B ADP . . . E 2 -72.902 152.019 43.415 1 95.64 ? O2B ADP 701 A 1 HETATM 4 O O3B ADP . . . E 2 -70.659 153.068 44.023 1 86.09 ? O3B ADP 701 A 1 HETATM 5 P PA ADP . . . E 2 -70.25 150.374 45.063 1 85.48 ? PA ADP 701 A 1 HETATM 6 O O1A ADP . . . E 2 -69.161 151.385 45.317 1 83.17 ? O1A ADP 701 A 1 HETATM 7 O O2A ADP . . . E 2 -71.413 150.251 46.02 1 93.87 ? O2A ADP 701 A 1 HETATM 8 O O3A ADP . . . E 2 -70.871 150.632 43.595 1 90.13 ? O3A ADP 701 A 1 HETATM 9 O O5' ADP . . . E 2 -69.534 148.943 44.961 1 85.16 ? O5' ADP 701 A 1 HETATM 10 C C5' ADP . . . E 2 -70.316 147.773 44.754 1 99.7 ? C5' ADP 701 A 1 HETATM 11 C C4' ADP . . . E 2 -69.493 146.552 45.142 1 92.22 ? C4' ADP 701 A 1 HETATM 12 O O4' ADP . . . E 2 -68.556 146.252 44.104 1 99.02 ? O4' ADP 701 A 1 HETATM 13 C C3' ADP . . . E 2 -68.714 146.784 46.427 1 93.17 ? C3' ADP 701 A 1 HETATM 14 O O3' ADP . . . E 2 -68.981 145.732 47.361 1 113.55 ? O3' ADP 701 A 1 HETATM 15 C C2' ADP . . . E 2 -67.255 146.79 46.017 1 101.81 ? C2' ADP 701 A 1 HETATM 16 O O2' ADP . . . E 2 -66.473 145.978 46.901 1 106.58 ? O2' ADP 701 A 1 HETATM 17 C C1' ADP . . . E 2 -67.212 146.25 44.593 1 97.3 ? C1' ADP 701 A 1 HETATM 18 N N9 ADP . . . E 2 -66.38 147.105 43.706 1 95.74 ? N9 ADP 701 A 1 HETATM 19 C C8 ADP . . . E 2 -66.873 147.824 42.68 1 97.53 ? C8 ADP 701 A 1 HETATM 20 N N7 ADP . . . E 2 -65.887 148.504 42.043 1 89.22 ? N7 ADP 701 A 1 HETATM 21 C C5 ADP . . . E 2 -64.734 148.22 42.666 1 86 ? C5 ADP 701 A 1 HETATM 22 C C6 ADP . . . E 2 -63.318 148.611 42.495 1 84.84 ? C6 ADP 701 A 1 HETATM 23 N N6 ADP . . . E 2 -62.961 149.462 41.504 1 91.27 ? N6 ADP 701 A 1 HETATM 24 N N1 ADP . . . E 2 -62.414 148.092 43.354 1 89.44 ? N1 ADP 701 A 1 HETATM 25 C C2 ADP . . . E 2 -62.772 147.243 44.34 1 94.27 ? C2 ADP 701 A 1 HETATM 26 N N3 ADP . . . E 2 -64.046 146.851 44.548 1 90.47 ? N3 ADP 701 A 1 HETATM 27 C C4 ADP . . . E 2 -65.056 147.293 43.761 1 95.12 ? C4 ADP 701 A 1 HETATM 28 H "H5'1" ADP . . . E 2 -71.222 147.82 45.363 1 119.77 ? "H5'1" ADP 701 A 1 HETATM 29 H "H5'2" ADP . . . E 2 -70.611 147.704 43.705 1 119.77 ? "H5'2" ADP 701 A 1 HETATM 30 H H4' ADP . . . E 2 -70.172 145.7 45.29 1 110.8 ? H4' ADP 701 A 1 HETATM 31 H H3' ADP . . . E 2 -68.984 147.761 46.851 1 111.94 ? H3' ADP 701 A 1 HETATM 32 H H2' ADP . . . E 2 -66.884 147.825 46.022 1 122.3 ? H2' ADP 701 A 1 HETATM 33 H HO2' ADP . . . E 2 -66.527 146.334 47.799 1 128.02 ? HO2' ADP 701 A 1 HETATM 34 H H1' ADP . . . E 2 -66.817 145.224 44.61 1 116.89 ? H1' ADP 701 A 1 HETATM 35 H H8 ADP . . . E 2 -67.919 147.858 42.402 1 117.16 ? H8 ADP 701 A 1 HETATM 36 H HN61 ADP . . . E 2 -61.993 149.726 41.389 1 109.65 ? HN61 ADP 701 A 1 HETATM 37 H HN62 ADP . . . E 2 -63.662 149.831 40.878 1 109.65 ? HN62 ADP 701 A 1 HETATM 38 H H2 ADP . . . E 2 -62.001 146.862 44.998 1 113.25 ? H2 ADP 701 A 1 # _model_server_stats.io_time_ms 71 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 38 #