data_8DCG # _model_server_result.job_id rEG3MoJM7f392bT8W9ug1g _model_server_result.datetime_utc '2024-11-16 01:57:25' _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 8dcg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":501}' # _entry.id 8DCG # _exptl.entry_id 8DCG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 363.221 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-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 90 _cell.entry_id 8DCG _cell.length_a 143.56 _cell.length_b 143.56 _cell.length_c 80.301 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DCG _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall 'P 4cw' _symmetry.space_group_name_H-M 'P 43' # 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,JA 1 1 B,D,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,KA 2 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 ? 3 E N N ? 3 U N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 1 _pdbx_entity_branch_link.entity_branch_list_num_2 2 _pdbx_entity_branch_link.comp_id_1 GLC _pdbx_entity_branch_link.comp_id_2 FRU _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O2 _pdbx_entity_branch_link.leaving_atom_id_2 HO2 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 GLC 1 C 1 GLC A 502 SUC 2 n C FRU 2 C 2 FRU A 502 SUC 2 n D GLC 1 D 1 GLC B 502 SUC 2 n D FRU 2 D 2 FRU B 502 SUC # 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 covale ? covale1 A NE2 HIS 254 A HIS 234 1_555 E P 5GP . A 5GP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.653 ? covale ? covale2 B NE2 HIS 254 B HIS 234 1_555 U P 5GP . B 5GP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.652 ? covale ? covale3 C C1 GLC . C GLC 1 1_555 C O2 FRU . C FRU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.414 ? covale ? covale4 D C1 GLC . D GLC 1 1_555 D O2 FRU . D FRU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? # _chem_comp.formula 'C10 H14 N5 O8 P' _chem_comp.formula_weight 363.221 _chem_comp.id 5GP _chem_comp.mon_nstd_flag . _chem_comp.name "GUANOSINE-5'-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 5GP doub 1 n n P O2P 5GP sing 2 n n P O3P 5GP sing 3 n n P O5' 5GP sing 4 n n O2P HOP2 5GP sing 5 n n O3P HOP3 5GP sing 6 n n O5' C5' 5GP sing 7 n n C5' C4' 5GP sing 8 n n C5' "H5'1" 5GP sing 9 n n C5' "H5'2" 5GP sing 10 n n C4' O4' 5GP sing 11 n n C4' C3' 5GP sing 12 n n C4' H4' 5GP sing 13 n n O4' C1' 5GP sing 14 n n C3' O3' 5GP sing 15 n n C3' C2' 5GP sing 16 n n C3' H3' 5GP sing 17 n n O3' HO3' 5GP sing 18 n n C2' O2' 5GP sing 19 n n C2' C1' 5GP sing 20 n n C2' H2' 5GP sing 21 n n O2' HO2' 5GP sing 22 n n C1' N9 5GP sing 23 n n C1' H1' 5GP sing 24 n n N9 C8 5GP sing 25 n y N9 C4 5GP sing 26 n y C8 N7 5GP doub 27 n y C8 H8 5GP sing 28 n n N7 C5 5GP sing 29 n y C5 C6 5GP sing 30 n n C5 C4 5GP doub 31 n y C6 O6 5GP doub 32 n n C6 N1 5GP sing 33 n n N1 C2 5GP sing 34 n n N1 HN1 5GP sing 35 n n C2 N2 5GP sing 36 n n C2 N3 5GP doub 37 n n N2 HN21 5GP sing 38 n n N2 HN22 5GP sing 39 n n N3 C4 5GP sing 40 n n # _atom_sites.entry_id 8DCG _atom_sites.fract_transf_matrix[1][1] 0.006966 _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] 0.006966 _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] 0.012453 _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 5GP A 1 501 501 5GP 5GP . F 4 SO4 A 1 502 1 SO4 SO4 . G 4 SO4 A 1 503 2 SO4 SO4 . H 4 SO4 A 1 504 3 SO4 SO4 . I 4 SO4 A 1 505 6 SO4 SO4 . J 4 SO4 A 1 506 8 SO4 SO4 . K 4 SO4 A 1 507 9 SO4 SO4 . L 4 SO4 A 1 508 10 SO4 SO4 . M 4 SO4 A 1 509 13 SO4 SO4 . N 4 SO4 A 1 510 16 SO4 SO4 . O 4 SO4 A 1 511 20 SO4 SO4 . P 4 SO4 A 1 512 21 SO4 SO4 . Q 4 SO4 A 1 513 22 SO4 SO4 . R 4 SO4 A 1 514 23 SO4 SO4 . S 5 CL A 1 515 3 CL CL . T 5 CL A 1 516 4 CL CL . U 3 5GP B 1 501 501 5GP 5GP . V 4 SO4 B 1 502 4 SO4 SO4 . W 4 SO4 B 1 503 5 SO4 SO4 . X 4 SO4 B 1 504 7 SO4 SO4 . Y 4 SO4 B 1 505 11 SO4 SO4 . Z 4 SO4 B 1 506 12 SO4 SO4 . AA 4 SO4 B 1 507 14 SO4 SO4 . BA 4 SO4 B 1 508 15 SO4 SO4 . CA 4 SO4 B 1 509 17 SO4 SO4 . DA 4 SO4 B 1 510 18 SO4 SO4 . EA 4 SO4 B 1 511 19 SO4 SO4 . FA 4 SO4 B 1 512 24 SO4 SO4 . GA 4 SO4 B 1 513 25 SO4 SO4 . HA 5 CL B 1 514 1 CL CL . IA 5 CL B 1 515 2 CL CL . JA 6 HOH A 1 601 1 HOH HOH . JA 6 HOH A 2 602 5 HOH HOH . JA 6 HOH A 3 603 3 HOH HOH . JA 6 HOH A 4 604 48 HOH HOH . JA 6 HOH A 5 605 32 HOH HOH . JA 6 HOH A 6 606 70 HOH HOH . JA 6 HOH A 7 607 79 HOH HOH . JA 6 HOH A 8 608 77 HOH HOH . JA 6 HOH A 9 609 64 HOH HOH . JA 6 HOH A 10 610 25 HOH HOH . JA 6 HOH A 11 611 65 HOH HOH . JA 6 HOH A 12 612 47 HOH HOH . JA 6 HOH A 13 613 30 HOH HOH . JA 6 HOH A 14 614 27 HOH HOH . JA 6 HOH A 15 615 26 HOH HOH . JA 6 HOH A 16 616 72 HOH HOH . JA 6 HOH A 17 617 54 HOH HOH . JA 6 HOH A 18 618 53 HOH HOH . JA 6 HOH A 19 619 12 HOH HOH . JA 6 HOH A 20 620 56 HOH HOH . JA 6 HOH A 21 621 23 HOH HOH . JA 6 HOH A 22 622 24 HOH HOH . JA 6 HOH A 23 623 45 HOH HOH . JA 6 HOH A 24 624 39 HOH HOH . JA 6 HOH A 25 625 28 HOH HOH . JA 6 HOH A 26 626 80 HOH HOH . JA 6 HOH A 27 627 2 HOH HOH . JA 6 HOH A 28 628 9 HOH HOH . JA 6 HOH A 29 629 11 HOH HOH . JA 6 HOH A 30 630 52 HOH HOH . JA 6 HOH A 31 631 4 HOH HOH . JA 6 HOH A 32 632 29 HOH HOH . JA 6 HOH A 33 633 69 HOH HOH . JA 6 HOH A 34 634 10 HOH HOH . JA 6 HOH A 35 635 76 HOH HOH . JA 6 HOH A 36 636 18 HOH HOH . JA 6 HOH A 37 637 46 HOH HOH . JA 6 HOH A 38 638 8 HOH HOH . JA 6 HOH A 39 639 67 HOH HOH . JA 6 HOH A 40 640 66 HOH HOH . JA 6 HOH A 41 641 57 HOH HOH . JA 6 HOH A 42 642 68 HOH HOH . JA 6 HOH A 43 643 75 HOH HOH . JA 6 HOH A 44 644 74 HOH HOH . KA 6 HOH B 1 601 73 HOH HOH . KA 6 HOH B 2 602 38 HOH HOH . KA 6 HOH B 3 603 7 HOH HOH . KA 6 HOH B 4 604 34 HOH HOH . KA 6 HOH B 5 605 15 HOH HOH . KA 6 HOH B 6 606 63 HOH HOH . KA 6 HOH B 7 607 20 HOH HOH . KA 6 HOH B 8 608 21 HOH HOH . KA 6 HOH B 9 609 78 HOH HOH . KA 6 HOH B 10 610 16 HOH HOH . KA 6 HOH B 11 611 17 HOH HOH . KA 6 HOH B 12 612 40 HOH HOH . KA 6 HOH B 13 613 13 HOH HOH . KA 6 HOH B 14 614 49 HOH HOH . KA 6 HOH B 15 615 58 HOH HOH . KA 6 HOH B 16 616 62 HOH HOH . KA 6 HOH B 17 617 31 HOH HOH . KA 6 HOH B 18 618 33 HOH HOH . KA 6 HOH B 19 619 60 HOH HOH . KA 6 HOH B 20 620 14 HOH HOH . KA 6 HOH B 21 621 44 HOH HOH . KA 6 HOH B 22 622 42 HOH HOH . KA 6 HOH B 23 623 50 HOH HOH . KA 6 HOH B 24 624 36 HOH HOH . KA 6 HOH B 25 625 37 HOH HOH . KA 6 HOH B 26 626 6 HOH HOH . KA 6 HOH B 27 627 43 HOH HOH . KA 6 HOH B 28 628 19 HOH HOH . KA 6 HOH B 29 629 41 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 5GP . . . U 3 20.54 -31.229 -21.175 0.79 73.41 ? P 5GP 501 B 1 HETATM 2 O O1P 5GP . . . U 3 19.807 -31.173 -22.498 0.79 55.7 ? O1P 5GP 501 B 1 HETATM 3 O O3P 5GP . . . U 3 22.005 -31.65 -21.204 0.79 64.76 ? O3P 5GP 501 B 1 HETATM 4 O O5' 5GP . . . U 3 20.523 -29.688 -20.702 0.79 61.56 ? O5' 5GP 501 B 1 HETATM 5 C C5' 5GP . . . U 3 21.643 -29.19 -19.939 0.79 62.4 ? C5' 5GP 501 B 1 HETATM 6 C C4' 5GP . . . U 3 21.241 -27.927 -19.221 0.79 59.59 ? C4' 5GP 501 B 1 HETATM 7 O O4' 5GP . . . U 3 20.277 -28.23 -18.184 0.79 58.28 ? O4' 5GP 501 B 1 HETATM 8 C C3' 5GP . . . U 3 22.359 -27.207 -18.468 0.79 59 ? C3' 5GP 501 B 1 HETATM 9 O O3' 5GP . . . U 3 23.127 -26.423 -19.369 0.79 57.66 ? O3' 5GP 501 B 1 HETATM 10 C C2' 5GP . . . U 3 21.575 -26.373 -17.452 0.79 57.18 ? C2' 5GP 501 B 1 HETATM 11 O O2' 5GP . . . U 3 21.178 -25.132 -17.99 0.79 53.64 ? O2' 5GP 501 B 1 HETATM 12 C C1' 5GP . . . U 3 20.354 -27.251 -17.172 0.79 56.89 ? C1' 5GP 501 B 1 HETATM 13 N N9 5GP . . . U 3 20.394 -27.944 -15.892 0.79 63.08 ? N9 5GP 501 B 1 HETATM 14 C C8 5GP . . . U 3 21.409 -28.726 -15.393 0.79 60 ? C8 5GP 501 B 1 HETATM 15 N N7 5GP . . . U 3 21.138 -29.23 -14.213 0.79 58.71 ? N7 5GP 501 B 1 HETATM 16 C C5 5GP . . . U 3 19.858 -28.763 -13.925 0.79 60.34 ? C5 5GP 501 B 1 HETATM 17 C C6 5GP . . . U 3 19.032 -28.987 -12.793 0.79 60.71 ? C6 5GP 501 B 1 HETATM 18 O O6 5GP . . . U 3 19.268 -29.673 -11.787 0.79 63.67 ? O6 5GP 501 B 1 HETATM 19 N N1 5GP . . . U 3 17.8 -28.342 -12.929 0.79 59.3 ? N1 5GP 501 B 1 HETATM 20 C C2 5GP . . . U 3 17.418 -27.563 -13.994 0.79 58.74 ? C2 5GP 501 B 1 HETATM 21 N N2 5GP . . . U 3 16.197 -27.013 -13.93 0.79 57.25 ? N2 5GP 501 B 1 HETATM 22 N N3 5GP . . . U 3 18.196 -27.339 -15.053 0.79 57.98 ? N3 5GP 501 B 1 HETATM 23 C C4 5GP . . . U 3 19.39 -27.972 -14.953 0.79 59.28 ? C4 5GP 501 B 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 250 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 23 #