data_6A46 # _model_server_result.job_id 4-ZHnp2bQnE8EBQf1eOHbg _model_server_result.datetime_utc '2025-08-26 14:25:20' _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 6a46 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":303}' # _entry.id 6A46 # _exptl.entry_id 6A46 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 307.197 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYCYTIDINE-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 100.76 _cell.angle_gamma 90 _cell.entry_id 6A46 _cell.length_a 43.808 _cell.length_b 54.773 _cell.length_c 88.716 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6A46 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,E,F,G,H,I,J,K,L,M _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 # 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 G 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 A OD1 ASP 34 A ASP 14 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.79 ? metalc ? metalc2 A OD2 ASP 34 A ASP 14 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? metalc ? metalc3 A OE1 GLU 36 A GLU 16 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc4 A OD2 ASP 213 A ASP 193 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.89 ? metalc ? metalc5 C MG MG . A MG 301 1_555 E O1P DCM . A DCM 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.748 ? metalc ? metalc6 C MG MG . A MG 301 1_555 L O HOH . A HOH 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc7 C MG MG . A MG 301 1_555 L O HOH . A HOH 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc8 C MG MG . A MG 301 1_555 L O HOH . A HOH 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc9 C MG MG . A MG 301 1_555 L O HOH . A HOH 457 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc10 D MG MG . A MG 302 1_555 E O1P DCM . A DCM 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.734 ? metalc ? metalc11 D MG MG . A MG 302 1_555 E O2P DCM . A DCM 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.967 ? metalc ? metalc12 B OD1 ASP 34 B ASP 14 1_555 H MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.836 ? metalc ? metalc13 B OD1 ASP 34 B ASP 14 1_555 I MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.88 ? metalc ? metalc14 B OD2 ASP 34 B ASP 14 1_555 I MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? metalc ? metalc15 B OE2 GLU 36 B GLU 16 1_555 I MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc16 B OD2 ASP 213 B ASP 193 1_555 I MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? metalc ? metalc17 G O3P DCM . B DCM 301 1_555 H MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.929 ? metalc ? metalc18 G O3P DCM . B DCM 301 1_555 I MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.815 ? metalc ? metalc19 H MG MG . B MG 302 1_555 M O HOH . B HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc20 H MG MG . B MG 302 1_555 M O HOH . B HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc21 H MG MG . B MG 302 1_555 M O HOH . B HOH 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc22 H MG MG . B MG 302 1_555 M O HOH . B HOH 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? # _chem_comp.formula 'C9 H14 N3 O7 P' _chem_comp.formula_weight 307.197 _chem_comp.id DCM _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYCYTIDINE-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 N1 C2 DCM sing 83 n n N1 C6 DCM sing 84 n n N1 C1' DCM sing 85 n n C2 N3 DCM sing 86 n n C2 O2 DCM doub 87 n n N3 C4 DCM doub 88 n n C4 C5 DCM sing 89 n n C4 N4 DCM sing 90 n n C5 C6 DCM doub 91 n n C5 H5 DCM sing 92 n n C6 H6 DCM sing 93 n n N4 HN41 DCM sing 94 n n N4 HN42 DCM sing 95 n n C1' C2' DCM sing 96 n n C1' O4' DCM sing 97 n n C1' H1' DCM sing 98 n n C2' C3' DCM sing 99 n n C2' "H2'1" DCM sing 100 n n C2' "H2'2" DCM sing 101 n n C3' C4' DCM sing 102 n n C3' O3' DCM sing 103 n n C3' H3' DCM sing 104 n n C4' O4' DCM sing 105 n n C4' C5' DCM sing 106 n n C4' H4' DCM sing 107 n n O3' HO3' DCM sing 108 n n C5' O5' DCM sing 109 n n C5' "H5'1" DCM sing 110 n n C5' "H5'2" DCM sing 111 n n O5' P DCM sing 112 n n P O1P DCM doub 113 n n P O2P DCM sing 114 n n P O3P DCM sing 115 n n O2P HOP2 DCM sing 116 n n O3P HOP3 DCM sing 117 n n # _atom_sites.entry_id 6A46 _atom_sites.fract_transf_matrix[1][1] 0.022827 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004337 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018257 _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] 0.011474 _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 MG A 1 301 1 MG MO6 . D 2 MG A 1 302 1 MG MG . E 3 DCM A 1 303 2 DCM DCM . F 4 CA A 1 304 1 CA CA . G 3 DCM B 1 301 3 DCM DCM . H 2 MG B 1 302 1 MG MO6 . I 2 MG B 1 303 1 MG MG . J 4 CA B 1 304 1 CA CA . K 4 CA B 1 305 2 CA CA . L 5 HOH A 1 401 75 HOH HOH . L 5 HOH A 2 402 36 HOH HOH . L 5 HOH A 3 403 96 HOH HOH . L 5 HOH A 4 404 97 HOH HOH . L 5 HOH A 5 405 50 HOH HOH . L 5 HOH A 6 406 12 HOH HOH . L 5 HOH A 7 407 1 HOH MO6 . L 5 HOH A 8 408 78 HOH HOH . L 5 HOH A 9 409 92 HOH HOH . L 5 HOH A 10 410 13 HOH HOH . L 5 HOH A 11 411 46 HOH HOH . L 5 HOH A 12 412 1 HOH MO6 . L 5 HOH A 13 413 102 HOH HOH . L 5 HOH A 14 414 49 HOH HOH . L 5 HOH A 15 415 14 HOH HOH . L 5 HOH A 16 416 38 HOH HOH . L 5 HOH A 17 417 18 HOH HOH . L 5 HOH A 18 418 43 HOH HOH . L 5 HOH A 19 419 62 HOH HOH . L 5 HOH A 20 420 98 HOH HOH . L 5 HOH A 21 421 56 HOH HOH . L 5 HOH A 22 422 5 HOH HOH . L 5 HOH A 23 423 27 HOH HOH . L 5 HOH A 24 424 35 HOH HOH . L 5 HOH A 25 425 51 HOH HOH . L 5 HOH A 26 426 44 HOH HOH . L 5 HOH A 27 427 2 HOH HOH . L 5 HOH A 28 428 87 HOH HOH . L 5 HOH A 29 429 11 HOH HOH . L 5 HOH A 30 430 1 HOH MO6 . L 5 HOH A 31 431 70 HOH HOH . L 5 HOH A 32 432 59 HOH HOH . L 5 HOH A 33 433 30 HOH HOH . L 5 HOH A 34 434 84 HOH HOH . L 5 HOH A 35 435 10 HOH HOH . L 5 HOH A 36 436 52 HOH HOH . L 5 HOH A 37 437 67 HOH HOH . L 5 HOH A 38 438 24 HOH HOH . L 5 HOH A 39 439 93 HOH HOH . L 5 HOH A 40 440 47 HOH HOH . L 5 HOH A 41 441 45 HOH HOH . L 5 HOH A 42 442 39 HOH HOH . L 5 HOH A 43 443 61 HOH HOH . L 5 HOH A 44 444 74 HOH HOH . L 5 HOH A 45 445 90 HOH HOH . L 5 HOH A 46 446 37 HOH HOH . L 5 HOH A 47 447 25 HOH HOH . L 5 HOH A 48 448 71 HOH HOH . L 5 HOH A 49 449 57 HOH HOH . L 5 HOH A 50 450 82 HOH HOH . L 5 HOH A 51 451 8 HOH HOH . L 5 HOH A 52 452 100 HOH HOH . L 5 HOH A 53 453 48 HOH HOH . L 5 HOH A 54 454 32 HOH HOH . L 5 HOH A 55 455 17 HOH HOH . L 5 HOH A 56 456 103 HOH HOH . L 5 HOH A 57 457 1 HOH MO6 . L 5 HOH A 58 458 99 HOH HOH . L 5 HOH A 59 459 41 HOH HOH . L 5 HOH A 60 460 85 HOH HOH . L 5 HOH A 61 461 20 HOH HOH . L 5 HOH A 62 462 34 HOH HOH . L 5 HOH A 63 463 58 HOH HOH . L 5 HOH A 64 464 23 HOH HOH . L 5 HOH A 65 465 15 HOH HOH . L 5 HOH A 66 466 60 HOH HOH . L 5 HOH A 67 467 29 HOH HOH . L 5 HOH A 68 468 31 HOH HOH . L 5 HOH A 69 469 86 HOH HOH . L 5 HOH A 70 470 76 HOH HOH . L 5 HOH A 71 471 88 HOH HOH . L 5 HOH A 72 472 54 HOH HOH . L 5 HOH A 73 473 55 HOH HOH . L 5 HOH A 74 474 73 HOH HOH . L 5 HOH A 75 475 83 HOH HOH . L 5 HOH A 76 476 79 HOH HOH . L 5 HOH A 77 477 64 HOH HOH . L 5 HOH A 78 478 94 HOH HOH . M 5 HOH B 1 401 1 HOH MO6 . M 5 HOH B 2 402 33 HOH HOH . M 5 HOH B 3 403 65 HOH HOH . M 5 HOH B 4 404 1 HOH MO6 . M 5 HOH B 5 405 77 HOH HOH . M 5 HOH B 6 406 53 HOH HOH . M 5 HOH B 7 407 28 HOH HOH . M 5 HOH B 8 408 95 HOH HOH . M 5 HOH B 9 409 1 HOH MO6 . M 5 HOH B 10 410 42 HOH HOH . M 5 HOH B 11 411 1 HOH HOH . M 5 HOH B 12 412 22 HOH HOH . M 5 HOH B 13 413 72 HOH HOH . M 5 HOH B 14 414 1 HOH MO6 . M 5 HOH B 15 415 69 HOH HOH . M 5 HOH B 16 416 80 HOH HOH . M 5 HOH B 17 417 40 HOH HOH . M 5 HOH B 18 418 101 HOH HOH . M 5 HOH B 19 419 9 HOH HOH . M 5 HOH B 20 420 63 HOH HOH . M 5 HOH B 21 421 26 HOH HOH . M 5 HOH B 22 422 6 HOH HOH . M 5 HOH B 23 423 4 HOH HOH . M 5 HOH B 24 424 81 HOH HOH . M 5 HOH B 25 425 66 HOH HOH . M 5 HOH B 26 426 21 HOH HOH . M 5 HOH B 27 427 19 HOH HOH . M 5 HOH B 28 428 3 HOH HOH . M 5 HOH B 29 429 16 HOH HOH . M 5 HOH B 30 430 91 HOH HOH . M 5 HOH B 31 431 7 HOH HOH . M 5 HOH B 32 432 89 HOH HOH . M 5 HOH B 33 433 68 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 N N1 DCM . . . E 3 1.469 19.682 14.016 1 42.94 ? N1 DCM 303 A 1 HETATM 2 C C2 DCM . . . E 3 1.35 21.099 14.385 1 44.86 ? C2 DCM 303 A 1 HETATM 3 N N3 DCM . . . E 3 0.094 21.821 14.124 1 45.56 ? N3 DCM 303 A 1 HETATM 4 C C4 DCM . . . E 3 -0.995 21.155 13.524 1 45.76 ? C4 DCM 303 A 1 HETATM 5 C C5 DCM . . . E 3 -0.877 19.744 13.156 1 44.64 ? C5 DCM 303 A 1 HETATM 6 C C6 DCM . . . E 3 0.368 19.02 13.411 1 43.69 ? C6 DCM 303 A 1 HETATM 7 O O2 DCM . . . E 3 2.27 21.663 14.894 1 47.2 ? O2 DCM 303 A 1 HETATM 8 N N4 DCM . . . E 3 -2.223 21.857 13.267 1 46.8 ? N4 DCM 303 A 1 HETATM 9 C C1' DCM . . . E 3 2.691 18.963 14.263 1 42.75 ? C1' DCM 303 A 1 HETATM 10 C C2' DCM . . . E 3 2.651 18.357 15.748 1 44.1 ? C2' DCM 303 A 1 HETATM 11 C C3' DCM . . . E 3 2.852 17.081 15.684 1 42.92 ? C3' DCM 303 A 1 HETATM 12 C C4' DCM . . . E 3 3.105 16.72 14.216 1 42.05 ? C4' DCM 303 A 1 HETATM 13 O O4' DCM . . . E 3 2.797 17.987 13.423 1 41.6 ? O4' DCM 303 A 1 HETATM 14 O O3' DCM . . . E 3 4.057 16.74 16.514 1 42.87 ? O3' DCM 303 A 1 HETATM 15 C C5' DCM . . . E 3 2.252 15.641 13.796 1 41.18 ? C5' DCM 303 A 1 HETATM 16 O O5' DCM . . . E 3 0.897 15.992 14.048 1 43.13 ? O5' DCM 303 A 1 HETATM 17 P P DCM . . . E 3 -0.154 14.897 14.663 1 96.99 ? P DCM 303 A 1 HETATM 18 O O1P DCM . . . E 3 -0.105 13.617 13.89 1 95.56 ? O1P DCM 303 A 1 HETATM 19 O O2P DCM . . . E 3 0.187 14.606 16.119 1 97.44 ? O2P DCM 303 A 1 HETATM 20 O O3P DCM . . . E 3 -1.536 15.453 14.568 1 99.08 ? O3P DCM 303 A 1 HETATM 21 H H5 DCM . . . E 3 -1.635 19.284 12.738 1 53.57 ? H5 DCM 303 A 1 HETATM 22 H H6 DCM . . . E 3 0.444 18.057 13.158 1 52.43 ? H6 DCM 303 A 1 HETATM 23 H HN41 DCM . . . E 3 -2.304 22.742 13.496 1 56.16 ? HN41 DCM 303 A 1 HETATM 24 H HN42 DCM . . . E 3 -2.938 21.412 12.87 1 56.16 ? HN42 DCM 303 A 1 HETATM 25 H H1' DCM . . . E 3 3.456 19.564 14.17 1 51.3 ? H1' DCM 303 A 1 HETATM 26 H "H2'1" DCM . . . E 3 3.351 18.772 16.289 1 52.92 ? "H2'1" DCM 303 A 1 HETATM 27 H "H2'2" DCM . . . E 3 1.765 18.535 16.156 1 52.92 ? "H2'2" DCM 303 A 1 HETATM 28 H H3' DCM . . . E 3 2.074 16.605 16.015 1 51.5 ? H3' DCM 303 A 1 HETATM 29 H H4' DCM . . . E 3 4.037 16.473 14.092 1 50.45 ? H4' DCM 303 A 1 HETATM 30 H "H5'1" DCM . . . E 3 2.372 15.47 12.865 1 49.42 ? "H5'1" DCM 303 A 1 HETATM 31 H "H5'2" DCM . . . E 3 2.473 14.853 14.293 1 49.42 ? "H5'2" DCM 303 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #