data_4JS2 # _model_server_result.job_id YyAZT0t-5yRXJzugM0lkxQ _model_server_result.datetime_utc '2024-11-18 06:32:01' _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 4js2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":511}' # _entry.id 4JS2 # _exptl.entry_id 4JS2 _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 1 _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 4JS2 _cell.length_a 64.027 _cell.length_b 64.027 _cell.length_c 160.571 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JS2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 2 5 4 NAG MAN C1 O1 . O2 HO2 . sing 5 ? 2 6 5 GAL NAG C1 O1 . O4 HO4 . sing 6 ? 2 7 3 MAN BMA C1 O1 . O6 HO6 . sing 7 ? 2 8 7 NAG MAN C1 O1 . O2 HO2 . sing 8 ? 2 9 8 GAL NAG C1 O1 . O4 HO4 . sing 9 ? 2 10 1 FUL NAG C1 O1 . O6 HO6 . 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 B NAG 1 B 1 NAG A 450 NAG 2 n B NAG 2 B 2 NAG A 451 NAG 2 n B BMA 3 B 3 BMA A 452 BMA 2 n B MAN 4 B 4 MAN A 453 MAN 2 n B NAG 5 B 5 NAG A 454 NAG 2 n B GAL 6 B 6 GAL A 455 GAL 2 n B MAN 7 B 7 MAN A 456 MAN 2 n B NAG 8 B 8 NAG A 457 NAG 2 n B GAL 9 B 9 GAL A 458 GAL 2 n B FUL 10 B 10 FUL A 460 FUC # 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 54 A CYS 142 1_555 A SG CYS 318 A CYS 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 A SG CYS 96 A CYS 184 1_555 A SG CYS 247 A CYS 335 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 A SG CYS 265 A CYS 353 1_555 A SG CYS 276 A CYS 364 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? covale ? covale1 A ND2 ASN 61 A ASN 149 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale3 B O6 NAG . B NAG 1 1_555 B C1 FUL . B FUL 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.025 ? covale ? covale4 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale5 B O3 BMA . B BMA 3 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale6 B O6 BMA . B BMA 3 1_555 B C1 MAN . B MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale7 B O2 MAN . B MAN 4 1_555 B C1 NAG . B NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 ? covale ? covale8 B O4 NAG . B NAG 5 1_555 B C1 GAL . B GAL 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale9 B O2 MAN . B MAN 7 1_555 B C1 NAG . B NAG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale10 B O4 NAG . B NAG 8 1_555 B C1 GAL . B GAL 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? # _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 94 n n O3P HOP3 C5P sing 95 n n P O1P C5P doub 96 n n P O2P C5P sing 97 n n P O5' C5P sing 98 n n O2P HOP2 C5P sing 99 n n O5' C5' C5P sing 100 n n C5' C4' C5P sing 101 n n C5' "H5'1" C5P sing 102 n n C5' "H5'2" C5P sing 103 n n C4' O4' C5P sing 104 n n C4' C3' C5P sing 105 n n C4' H4' C5P sing 106 n n O4' C1' C5P sing 107 n n C3' O3' C5P sing 108 n n C3' C2' C5P sing 109 n n C3' H3' C5P sing 110 n n O3' HO3' C5P sing 111 n n C2' O2' C5P sing 112 n n C2' C1' C5P sing 113 n n C2' "H2'1" C5P sing 114 n n O2' HO2' C5P sing 115 n n C1' N1 C5P sing 116 n n C1' H1' C5P sing 117 n n N1 C2 C5P sing 118 n n N1 C6 C5P sing 119 n n C2 N3 C5P sing 120 n n C2 O2 C5P doub 121 n n N3 C4 C5P doub 122 n n C4 C5 C5P sing 123 n n C4 N4 C5P sing 124 n n C5 C6 C5P doub 125 n n C5 H5 C5P sing 126 n n C6 H6 C5P sing 127 n n N4 HN41 C5P sing 128 n n N4 HN42 C5P sing 129 n n # _atom_sites.entry_id 4JS2 _atom_sites.fract_transf_matrix[1][1] 0.015618 _atom_sites.fract_transf_matrix[1][2] 0.009017 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018035 _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] 0.006228 _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 3 C5P A 1 511 500 C5P C . D 4 HOH A 1 601 1 HOH HOH . D 4 HOH A 2 602 2 HOH HOH . D 4 HOH A 3 603 3 HOH HOH . D 4 HOH A 4 604 4 HOH HOH . D 4 HOH A 5 605 5 HOH HOH . D 4 HOH A 6 606 6 HOH HOH . D 4 HOH A 7 607 7 HOH HOH . D 4 HOH A 8 608 8 HOH HOH . D 4 HOH A 9 609 9 HOH HOH . D 4 HOH A 10 610 10 HOH HOH . D 4 HOH A 11 611 11 HOH HOH . D 4 HOH A 12 612 12 HOH HOH . D 4 HOH A 13 613 13 HOH HOH . D 4 HOH A 14 614 14 HOH HOH . D 4 HOH A 15 615 15 HOH HOH . D 4 HOH A 16 616 16 HOH HOH . D 4 HOH A 17 617 17 HOH HOH . D 4 HOH A 18 618 18 HOH HOH . D 4 HOH A 19 619 19 HOH HOH . D 4 HOH A 20 620 20 HOH HOH . D 4 HOH A 21 621 21 HOH HOH . D 4 HOH A 22 622 22 HOH HOH . D 4 HOH A 23 623 23 HOH HOH . D 4 HOH A 24 624 24 HOH HOH . D 4 HOH A 25 625 25 HOH HOH . D 4 HOH A 26 626 26 HOH HOH . D 4 HOH A 27 627 27 HOH HOH . D 4 HOH A 28 628 28 HOH HOH . D 4 HOH A 29 629 29 HOH HOH . D 4 HOH A 30 630 30 HOH HOH . D 4 HOH A 31 631 31 HOH HOH . D 4 HOH A 32 632 32 HOH HOH . D 4 HOH A 33 633 33 HOH HOH . D 4 HOH A 34 634 34 HOH HOH . D 4 HOH A 35 635 35 HOH HOH . D 4 HOH A 36 636 36 HOH HOH . D 4 HOH A 37 637 37 HOH HOH . D 4 HOH A 38 638 38 HOH HOH . D 4 HOH A 39 639 39 HOH HOH . D 4 HOH A 40 640 40 HOH HOH . D 4 HOH A 41 641 41 HOH HOH . D 4 HOH A 42 642 42 HOH HOH . D 4 HOH A 43 643 43 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 . . . C 3 8.07 51.629 35.392 1 58.31 ? O3P C5P 511 A 1 HETATM 2 P P C5P . . . C 3 6.561 51.979 35.369 1 58.91 ? P C5P 511 A 1 HETATM 3 O O1P C5P . . . C 3 6.298 53.492 35.614 1 56.61 ? O1P C5P 511 A 1 HETATM 4 O O2P C5P . . . C 3 5.809 51.371 34.136 1 72.13 ? O2P C5P 511 A 1 HETATM 5 O O5' C5P . . . C 3 5.939 51.175 36.589 1 60.74 ? O5' C5P 511 A 1 HETATM 6 C C5' C5P . . . C 3 5.862 49.759 36.541 1 60.01 ? C5' C5P 511 A 1 HETATM 7 C C4' C5P . . . C 3 4.452 49.315 36.773 1 60.17 ? C4' C5P 511 A 1 HETATM 8 O O4' C5P . . . C 3 4.169 49.383 38.186 1 61.77 ? O4' C5P 511 A 1 HETATM 9 C C3' C5P . . . C 3 3.398 50.219 36.164 1 61.58 ? C3' C5P 511 A 1 HETATM 10 O O3' C5P . . . C 3 3.199 49.957 34.788 1 60.88 ? O3' C5P 511 A 1 HETATM 11 C C2' C5P . . . C 3 2.171 49.926 37.014 1 61.74 ? C2' C5P 511 A 1 HETATM 12 O O2' C5P . . . C 3 1.564 48.719 36.571 1 62.32 ? O2' C5P 511 A 1 HETATM 13 C C1' C5P . . . C 3 2.801 49.658 38.383 1 60.79 ? C1' C5P 511 A 1 HETATM 14 N N1 C5P . . . C 3 2.695 50.8 39.312 1 60.05 ? N1 C5P 511 A 1 HETATM 15 C C2 C5P . . . C 3 1.536 50.891 40.144 1 58.93 ? C2 C5P 511 A 1 HETATM 16 N N3 C5P . . . C 3 1.457 51.934 41.017 1 58.94 ? N3 C5P 511 A 1 HETATM 17 C C4 C5P . . . C 3 2.42 52.819 41.105 1 58.85 ? C4 C5P 511 A 1 HETATM 18 C C5 C5P . . . C 3 3.606 52.771 40.298 1 58.61 ? C5 C5P 511 A 1 HETATM 19 C C6 C5P . . . C 3 3.74 51.754 39.409 1 58.95 ? C6 C5P 511 A 1 HETATM 20 O O2 C5P . . . C 3 0.639 50.012 40.02 1 58.54 ? O2 C5P 511 A 1 HETATM 21 N N4 C5P . . . C 3 2.27 53.839 42.036 1 58.33 ? N4 C5P 511 A 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 382 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 21 #