data_8CSB # _model_server_result.job_id U9OPiY_rAjDbsNyL3MCRzg _model_server_result.datetime_utc '2024-11-16 16:56:43' _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 8csb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":504}' # _entry.id 8CSB # _exptl.entry_id 8CSB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 323.197 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-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 8CSB _cell.length_a 92.71 _cell.length_b 157.44 _cell.length_c 120.06 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8CSB _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall 'C 2c 2' _symmetry.space_group_name_H-M 'C 2 2 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,K 1 1,2 B,H,I,J,L 2 1,2 # 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,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 60.03 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 J 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 covale ? covale1 A C HIS 28 A HIS 27 1_555 A N CSO 29 A CSO 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C CSO 29 A CSO 28 1_555 A N ALA 30 A ALA 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale3 B C HIS 28 B HIS 27 1_555 B N CSO 29 B CSO 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale4 B C CSO 29 B CSO 28 1_555 B N ALA 30 B ALA 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? # _chem_comp.formula 'C9 H14 N3 O8 P' _chem_comp.formula_weight 323.197 _chem_comp.id C5P _chem_comp.mon_nstd_flag . _chem_comp.name "CYTIDINE-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 O3P P C5P sing 70 n n O3P HOP3 C5P sing 71 n n P O1P C5P doub 72 n n P O2P C5P sing 73 n n P O5' C5P sing 74 n n O2P HOP2 C5P sing 75 n n O5' C5' C5P sing 76 n n C5' C4' C5P sing 77 n n C5' "H5'1" C5P sing 78 n n C5' "H5'2" C5P sing 79 n n C4' O4' C5P sing 80 n n C4' C3' C5P sing 81 n n C4' H4' C5P sing 82 n n O4' C1' C5P sing 83 n n C3' O3' C5P sing 84 n n C3' C2' C5P sing 85 n n C3' H3' C5P sing 86 n n O3' HO3' C5P sing 87 n n C2' O2' C5P sing 88 n n C2' C1' C5P sing 89 n n C2' "H2'1" C5P sing 90 n n O2' HO2' C5P sing 91 n n C1' N1 C5P sing 92 n n C1' H1' C5P sing 93 n n N1 C2 C5P sing 94 n n N1 C6 C5P sing 95 n n C2 N3 C5P sing 96 n n C2 O2 C5P doub 97 n n N3 C4 C5P doub 98 n n C4 C5 C5P sing 99 n n C4 N4 C5P sing 100 n n C5 C6 C5P doub 101 n n C5 H5 C5P sing 102 n n C6 H6 C5P sing 103 n n N4 HN41 C5P sing 104 n n N4 HN42 C5P sing 105 n n # _atom_sites.entry_id 8CSB _atom_sites.fract_transf_matrix[1][1] 0.010786 _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] 0.006352 _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] 0.008329 _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 C 2 PO4 A 1 501 1 PO4 PO4 . D 2 PO4 A 1 502 3 PO4 PO4 . E 2 PO4 A 1 503 4 PO4 PO4 . F 3 C5P A 1 504 1 C5P C5P . G 4 CMK A 1 505 2 CMK CMK . H 2 PO4 B 1 501 2 PO4 PO4 . I 4 CMK B 1 502 1 CMK CMK . J 3 C5P B 1 503 2 C5P C5P . K 5 HOH A 1 601 82 HOH HOH . K 5 HOH A 2 602 34 HOH HOH . K 5 HOH A 3 603 37 HOH HOH . K 5 HOH A 4 604 78 HOH HOH . K 5 HOH A 5 605 76 HOH HOH . K 5 HOH A 6 606 33 HOH HOH . K 5 HOH A 7 607 55 HOH HOH . K 5 HOH A 8 608 74 HOH HOH . K 5 HOH A 9 609 69 HOH HOH . K 5 HOH A 10 610 36 HOH HOH . K 5 HOH A 11 611 39 HOH HOH . K 5 HOH A 12 612 62 HOH HOH . K 5 HOH A 13 613 79 HOH HOH . K 5 HOH A 14 614 51 HOH HOH . K 5 HOH A 15 615 21 HOH HOH . K 5 HOH A 16 616 9 HOH HOH . K 5 HOH A 17 617 68 HOH HOH . K 5 HOH A 18 618 44 HOH HOH . K 5 HOH A 19 619 27 HOH HOH . K 5 HOH A 20 620 3 HOH HOH . K 5 HOH A 21 621 30 HOH HOH . K 5 HOH A 22 622 8 HOH HOH . K 5 HOH A 23 623 6 HOH HOH . K 5 HOH A 24 624 73 HOH HOH . K 5 HOH A 25 625 53 HOH HOH . K 5 HOH A 26 626 10 HOH HOH . K 5 HOH A 27 627 49 HOH HOH . K 5 HOH A 28 628 28 HOH HOH . K 5 HOH A 29 629 59 HOH HOH . K 5 HOH A 30 630 20 HOH HOH . K 5 HOH A 31 631 18 HOH HOH . K 5 HOH A 32 632 81 HOH HOH . K 5 HOH A 33 633 56 HOH HOH . K 5 HOH A 34 634 43 HOH HOH . K 5 HOH A 35 635 50 HOH HOH . K 5 HOH A 36 636 66 HOH HOH . K 5 HOH A 37 637 19 HOH HOH . K 5 HOH A 38 638 31 HOH HOH . K 5 HOH A 39 639 58 HOH HOH . K 5 HOH A 40 640 54 HOH HOH . K 5 HOH A 41 641 67 HOH HOH . K 5 HOH A 42 642 83 HOH HOH . K 5 HOH A 43 643 64 HOH HOH . K 5 HOH A 44 644 71 HOH HOH . L 5 HOH B 1 601 75 HOH HOH . L 5 HOH B 2 602 80 HOH HOH . L 5 HOH B 3 603 48 HOH HOH . L 5 HOH B 4 604 13 HOH HOH . L 5 HOH B 5 605 1 HOH HOH . L 5 HOH B 6 606 63 HOH HOH . L 5 HOH B 7 607 57 HOH HOH . L 5 HOH B 8 608 23 HOH HOH . L 5 HOH B 9 609 46 HOH HOH . L 5 HOH B 10 610 61 HOH HOH . L 5 HOH B 11 611 16 HOH HOH . L 5 HOH B 12 612 35 HOH HOH . L 5 HOH B 13 613 25 HOH HOH . L 5 HOH B 14 614 32 HOH HOH . L 5 HOH B 15 615 5 HOH HOH . L 5 HOH B 16 616 17 HOH HOH . L 5 HOH B 17 617 12 HOH HOH . L 5 HOH B 18 618 2 HOH HOH . L 5 HOH B 19 619 14 HOH HOH . L 5 HOH B 20 620 41 HOH HOH . L 5 HOH B 21 621 4 HOH HOH . L 5 HOH B 22 622 38 HOH HOH . L 5 HOH B 23 623 26 HOH HOH . L 5 HOH B 24 624 52 HOH HOH . L 5 HOH B 25 625 72 HOH HOH . L 5 HOH B 26 626 7 HOH HOH . L 5 HOH B 27 627 45 HOH HOH . L 5 HOH B 28 628 85 HOH HOH . L 5 HOH B 29 629 70 HOH HOH . L 5 HOH B 30 630 40 HOH HOH . L 5 HOH B 31 631 47 HOH HOH . L 5 HOH B 32 632 84 HOH HOH . L 5 HOH B 33 633 22 HOH HOH . L 5 HOH B 34 634 11 HOH HOH . L 5 HOH B 35 635 60 HOH HOH . L 5 HOH B 36 636 15 HOH HOH . L 5 HOH B 37 637 24 HOH HOH . L 5 HOH B 38 638 77 HOH HOH . L 5 HOH B 39 639 42 HOH HOH . L 5 HOH B 40 640 65 HOH HOH . L 5 HOH B 41 641 29 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 O O3P C5P . B . F 3 11.747 21.354 21.639 0.31 57.59 ? O3P C5P 504 A 1 HETATM 2 P P C5P . B . F 3 13.154 21.431 22.159 0.31 59.45 ? P C5P 504 A 1 HETATM 3 O O1P C5P . B . F 3 13.995 22.552 21.636 0.31 61.65 ? O1P C5P 504 A 1 HETATM 4 O O2P C5P . B . F 3 13.354 21.104 23.604 0.31 72.3 ? O2P C5P 504 A 1 HETATM 5 O O5' C5P . B . F 3 13.99 19.993 21.135 0.31 59.61 ? O5' C5P 504 A 1 HETATM 6 C C5' C5P . B . F 3 15.113 19.371 21.516 0.31 59.68 ? C5' C5P 504 A 1 HETATM 7 C C4' C5P . B . F 3 15.069 17.814 21.235 0.31 58.34 ? C4' C5P 504 A 1 HETATM 8 O O4' C5P . B . F 3 13.983 17.088 21.801 0.31 58.7 ? O4' C5P 504 A 1 HETATM 9 C C3' C5P . B . F 3 14.887 17.626 19.649 0.31 57.73 ? C3' C5P 504 A 1 HETATM 10 O O3' C5P . B . F 3 16.003 17.756 18.839 0.31 56.81 ? O3' C5P 504 A 1 HETATM 11 C C2' C5P . B . F 3 14.361 16.163 19.588 0.31 57.22 ? C2' C5P 504 A 1 HETATM 12 O O2' C5P . B . F 3 15.48 15.364 19.647 0.31 57.53 ? O2' C5P 504 A 1 HETATM 13 C C1' C5P . B . F 3 13.499 16.079 20.931 0.31 57.32 ? C1' C5P 504 A 1 HETATM 14 N N1 C5P . B . F 3 11.982 16.423 20.755 0.31 57.08 ? N1 C5P 504 A 1 HETATM 15 C C2 C5P . B . F 3 11.098 15.382 20.246 0.31 68.41 ? C2 C5P 504 A 1 HETATM 16 N N3 C5P . B . F 3 9.705 15.759 20.109 0.31 59.13 ? N3 C5P 504 A 1 HETATM 17 C C4 C5P . B . F 3 9.205 16.963 20.424 0.31 57.2 ? C4 C5P 504 A 1 HETATM 18 C C5 C5P . B . F 3 10.132 18.016 20.959 0.31 56.96 ? C5 C5P 504 A 1 HETATM 19 C C6 C5P . B . F 3 11.479 17.687 21.104 0.31 57.56 ? C6 C5P 504 A 1 HETATM 20 O O2 C5P . B . F 3 11.549 14.299 19.959 0.31 58 ? O2 C5P 504 A 1 HETATM 21 N N4 C5P . B . F 3 7.781 17.2 20.234 0.31 55.59 ? N4 C5P 504 A 1 HETATM 22 H "H5'1" C5P . B . F 3 15.311 19.387 22.466 0.31 72.19 ? "H5'1" C5P 504 A 1 HETATM 23 H "H5'2" C5P . B . F 3 15.925 19.625 21.049 0.31 72.19 ? "H5'2" C5P 504 A 1 HETATM 24 H H4' C5P . B . F 3 15.798 17.341 21.667 0.31 70.59 ? H4' C5P 504 A 1 HETATM 25 H H3' C5P . B . F 3 14.072 17.98 19.26 0.31 69.85 ? H3' C5P 504 A 1 HETATM 26 H HO3' C5P . B . F 3 15.774 17.949 18.032 0.31 68.75 ? HO3' C5P 504 A 1 HETATM 27 H "H2'1" C5P . B . F 3 13.858 16.179 18.758 0.31 69.23 ? "H2'1" C5P 504 A 1 HETATM 28 H HO2' C5P . B . F 3 15.349 14.665 19.199 0.31 69.61 ? HO2' C5P 504 A 1 HETATM 29 H H1' C5P . B . F 3 13.613 15.145 21.166 0.31 69.36 ? H1' C5P 504 A 1 HETATM 30 H H5 C5P . B . F 3 9.786 18.851 21.177 0.31 68.93 ? H5 C5P 504 A 1 HETATM 31 H H6 C5P . B . F 3 12.106 18.287 21.438 0.31 69.65 ? H6 C5P 504 A 1 HETATM 32 H HN41 C5P . B . F 3 7.395 17.623 19.588 0.31 67.28 ? HN41 C5P 504 A 1 HETATM 33 H HN42 C5P . B . F 3 7.134 16.951 20.741 0.31 67.28 ? HN42 C5P 504 A 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 33 #