data_4HLQ # _model_server_result.job_id t9-uLkDpzRbSaur6aTTTXQ _model_server_result.datetime_utc '2025-02-05 15:45:27' _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 4hlq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"CA","auth_seq_id":202}' # _entry.id 4HLQ # _exptl.entry_id 4HLQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 5 _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 4HLQ _cell.length_a 88.17 _cell.length_b 118.64 _cell.length_c 290.11 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4HLQ _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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 PISA dimeric 2 author_and_software_defined_assembly 5 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,K,L,M,N,EA,FA 1 1 C,D,O,P,Q,R,GA,HA 2 1 E,F,S,T,U,V,W,IA,JA 3 1 G,H,X,Y,Z,KA,LA 4 1 I,J,AA,BA,CA,DA,MA,NA 5 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 M N N ? 5 Q N N ? 5 V N N ? 5 Y N N ? 5 CA 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 B OG SER 23 B SER 22 1_555 L MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc2 B OG1 THR 41 B THR 40 1_555 L MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc3 L MG MG . B MG 201 1_555 M O2B GDP . B GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? metalc ? metalc4 M O1B GDP . B GDP 202 1_555 N BE BEF . B BEF 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc5 D OG SER 23 D SER 22 1_555 P MG MG . D MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc6 D OG1 THR 41 D THR 40 1_555 P MG MG . D MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? metalc ? metalc7 Q O3B GDP . D GDP 202 1_555 R BE BEF . D BEF 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.599 ? metalc ? metalc8 F OG SER 23 F SER 22 1_555 U MG MG . F MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc9 F OG1 THR 41 F THR 40 1_555 U MG MG . F MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc10 U MG MG . F MG 201 1_555 V O3B GDP . F GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.715 ? metalc ? metalc11 V O2B GDP . F GDP 202 1_555 W BE BEF . F BEF 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.779 ? metalc ? metalc12 H OG SER 23 H SER 22 1_555 X MG MG . H MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc13 H OG1 THR 41 H THR 40 1_555 X MG MG . H MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc14 X MG MG . H MG 201 1_555 Y O3B GDP . H GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc15 X MG MG . H MG 201 1_555 Y O2B GDP . H GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? metalc ? metalc16 Y O2B GDP . H GDP 202 1_555 Z BE BEF . H BEF 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc17 J OG SER 23 J SER 22 1_555 BA MG MG . J MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? metalc ? metalc18 J OG1 THR 41 J THR 40 1_555 BA MG MG . J MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.704 ? metalc ? metalc19 BA MG MG . J MG 201 1_555 CA O3B GDP . J GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc20 CA O3B GDP . J GDP 202 1_555 DA BE BEF . J BEF 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.92 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 GDP doub 86 n n PB O2B GDP sing 87 n n PB O3B GDP sing 88 n n PB O3A GDP sing 89 n n O2B HOB2 GDP sing 90 n n O3B HOB3 GDP sing 91 n n O3A PA GDP sing 92 n n PA O1A GDP doub 93 n n PA O2A GDP sing 94 n n PA O5' GDP sing 95 n n O2A HOA2 GDP sing 96 n n O5' C5' GDP sing 97 n n C5' C4' GDP sing 98 n n C5' H5' GDP sing 99 n n C5' "H5''" GDP sing 100 n n C4' O4' GDP sing 101 n n C4' C3' GDP sing 102 n n C4' H4' GDP sing 103 n n O4' C1' GDP sing 104 n n C3' O3' GDP sing 105 n n C3' C2' GDP sing 106 n n C3' H3' GDP sing 107 n n O3' HO3' GDP sing 108 n n C2' O2' GDP sing 109 n n C2' C1' GDP sing 110 n n C2' H2' GDP sing 111 n n O2' HO2' GDP sing 112 n n C1' N9 GDP sing 113 n n C1' H1' GDP sing 114 n n N9 C8 GDP sing 115 n y N9 C4 GDP sing 116 n y C8 N7 GDP doub 117 n y C8 H8 GDP sing 118 n n N7 C5 GDP sing 119 n y C5 C6 GDP sing 120 n n C5 C4 GDP doub 121 n y C6 O6 GDP doub 122 n n C6 N1 GDP sing 123 n n N1 C2 GDP sing 124 n n N1 HN1 GDP sing 125 n n C2 N2 GDP sing 126 n n C2 N3 GDP doub 127 n n N2 HN21 GDP sing 128 n n N2 HN22 GDP sing 129 n n N3 C4 GDP sing 130 n n # _atom_sites.entry_id 4HLQ _atom_sites.fract_transf_matrix[1][1] 0.011342 _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] 0.008429 _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] 0.003447 _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 K 3 SO4 A 1 401 1 SO4 SO4 . L 4 MG B 1 201 1 MG MG . M 5 GDP B 1 202 1 GDP GDP . N 6 BEF B 1 203 1 BEF BEF . O 3 SO4 C 1 401 2 SO4 SO4 . P 4 MG D 1 201 2 MG MG . Q 5 GDP D 1 202 2 GDP GDP . R 6 BEF D 1 203 2 BEF BEF . S 3 SO4 E 1 401 3 SO4 SO4 . T 3 SO4 E 1 402 4 SO4 SO4 . U 4 MG F 1 201 3 MG MG . V 5 GDP F 1 202 3 GDP GDP . W 6 BEF F 1 203 3 BEF BEF . X 4 MG H 1 201 4 MG MG . Y 5 GDP H 1 202 4 GDP GDP . Z 6 BEF H 1 203 4 BEF BEF . AA 3 SO4 I 1 401 5 SO4 SO4 . BA 4 MG J 1 201 5 MG MG . CA 5 GDP J 1 202 5 GDP GDP . DA 6 BEF J 1 203 5 BEF BEF . EA 7 HOH A 1 501 9 HOH HOH . EA 7 HOH A 2 502 17 HOH HOH . EA 7 HOH A 3 503 19 HOH HOH . EA 7 HOH A 4 504 22 HOH HOH . EA 7 HOH A 5 505 26 HOH HOH . EA 7 HOH A 6 506 27 HOH HOH . EA 7 HOH A 7 507 40 HOH HOH . EA 7 HOH A 8 508 44 HOH HOH . EA 7 HOH A 9 509 47 HOH HOH . FA 7 HOH B 1 301 7 HOH HOH . FA 7 HOH B 2 302 11 HOH HOH . FA 7 HOH B 3 303 43 HOH HOH . FA 7 HOH B 4 304 45 HOH HOH . GA 7 HOH C 1 501 1 HOH HOH . GA 7 HOH C 2 502 10 HOH HOH . GA 7 HOH C 3 503 18 HOH HOH . GA 7 HOH C 4 504 20 HOH HOH . GA 7 HOH C 5 505 41 HOH HOH . GA 7 HOH C 6 506 42 HOH HOH . GA 7 HOH C 7 507 46 HOH HOH . HA 7 HOH D 1 301 8 HOH HOH . HA 7 HOH D 2 302 14 HOH HOH . HA 7 HOH D 3 303 31 HOH HOH . HA 7 HOH D 4 304 38 HOH HOH . IA 7 HOH E 1 501 2 HOH HOH . IA 7 HOH E 2 502 16 HOH HOH . IA 7 HOH E 3 503 21 HOH HOH . IA 7 HOH E 4 504 23 HOH HOH . IA 7 HOH E 5 505 25 HOH HOH . IA 7 HOH E 6 506 32 HOH HOH . IA 7 HOH E 7 507 37 HOH HOH . IA 7 HOH E 8 508 51 HOH HOH . JA 7 HOH F 1 301 13 HOH HOH . JA 7 HOH F 2 302 30 HOH HOH . JA 7 HOH F 3 303 48 HOH HOH . JA 7 HOH F 4 304 50 HOH HOH . KA 7 HOH G 1 401 3 HOH HOH . KA 7 HOH G 2 402 12 HOH HOH . KA 7 HOH G 3 403 24 HOH HOH . KA 7 HOH G 4 404 35 HOH HOH . LA 7 HOH H 1 301 28 HOH HOH . LA 7 HOH H 2 302 36 HOH HOH . MA 7 HOH I 1 501 4 HOH HOH . MA 7 HOH I 2 502 5 HOH HOH . MA 7 HOH I 3 503 6 HOH HOH . MA 7 HOH I 4 504 15 HOH HOH . MA 7 HOH I 5 505 33 HOH HOH . MA 7 HOH I 6 506 34 HOH HOH . MA 7 HOH I 7 507 49 HOH HOH . NA 7 HOH J 1 301 29 HOH HOH . NA 7 HOH J 2 302 39 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 GDP . . . CA 5 -42.096 61.809 -4.199 1 85.35 ? PB GDP 202 J 1 HETATM 2 O O1B GDP . . . CA 5 -41.086 61.413 -3.219 1 85.22 ? O1B GDP 202 J 1 HETATM 3 O O2B GDP . . . CA 5 -43.224 62.569 -3.632 1 84.79 ? O2B GDP 202 J 1 HETATM 4 O O3B GDP . . . CA 5 -42.494 60.758 -5.151 1 86 ? O3B GDP 202 J 1 HETATM 5 O O3A GDP . . . CA 5 -41.346 62.908 -5.077 1 86.35 ? O3A GDP 202 J 1 HETATM 6 P PA GDP . . . CA 5 -40.126 63.716 -4.408 1 87.41 ? PA GDP 202 J 1 HETATM 7 O O1A GDP . . . CA 5 -40.407 63.764 -2.963 1 87.45 ? O1A GDP 202 J 1 HETATM 8 O O2A GDP . . . CA 5 -38.845 63.168 -4.895 1 86.91 ? O2A GDP 202 J 1 HETATM 9 O O5' GDP . . . CA 5 -40.269 65.215 -4.927 1 88.42 ? O5' GDP 202 J 1 HETATM 10 C C5' GDP . . . CA 5 -39.535 66.141 -4.13 1 89.66 ? C5' GDP 202 J 1 HETATM 11 C C4' GDP . . . CA 5 -39.967 67.589 -4.322 1 90.38 ? C4' GDP 202 J 1 HETATM 12 O O4' GDP . . . CA 5 -40.018 68.245 -3.015 1 90.59 ? O4' GDP 202 J 1 HETATM 13 C C3' GDP . . . CA 5 -38.875 68.287 -5.103 1 90.76 ? C3' GDP 202 J 1 HETATM 14 O O3' GDP . . . CA 5 -39.415 69.453 -5.745 1 91.34 ? O3' GDP 202 J 1 HETATM 15 C C2' GDP . . . CA 5 -37.875 68.674 -4.029 1 90.94 ? C2' GDP 202 J 1 HETATM 16 O O2' GDP . . . CA 5 -37.171 69.854 -4.436 1 90.85 ? O2' GDP 202 J 1 HETATM 17 C C1' GDP . . . CA 5 -38.751 68.949 -2.788 1 91.3 ? C1' GDP 202 J 1 HETATM 18 N N9 GDP . . . CA 5 -38.095 68.507 -1.493 1 92.17 ? N9 GDP 202 J 1 HETATM 19 C C8 GDP . . . CA 5 -37.702 67.271 -1.184 1 92.44 ? C8 GDP 202 J 1 HETATM 20 N N7 GDP . . . CA 5 -37.174 67.288 0.037 1 92.73 ? N7 GDP 202 J 1 HETATM 21 C C5 GDP . . . CA 5 -37.237 68.536 0.501 1 92.93 ? C5 GDP 202 J 1 HETATM 22 C C6 GDP . . . CA 5 -36.845 69.072 1.665 1 93.05 ? C6 GDP 202 J 1 HETATM 23 O O6 GDP . . . CA 5 -36.321 68.382 2.541 1 93.27 ? O6 GDP 202 J 1 HETATM 24 N N1 GDP . . . CA 5 -37.03 70.441 1.897 1 92.85 ? N1 GDP 202 J 1 HETATM 25 C C2 GDP . . . CA 5 -37.626 71.211 0.894 1 92.59 ? C2 GDP 202 J 1 HETATM 26 N N2 GDP . . . CA 5 -37.825 72.515 1.071 1 92.54 ? N2 GDP 202 J 1 HETATM 27 N N3 GDP . . . CA 5 -37.998 70.615 -0.249 1 92.72 ? N3 GDP 202 J 1 HETATM 28 C C4 GDP . . . CA 5 -37.808 69.294 -0.447 1 92.67 ? C4 GDP 202 J 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 28 #