data_6TXR # _model_server_result.job_id '_kE_fQ69KFJKmFLHG_hXpA' _model_server_result.datetime_utc '2024-11-22 10:48:20' _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 6txr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"IA","auth_seq_id":406}' # _entry.id 6TXR # _exptl.entry_id 6TXR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 307.197 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 20 _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 6TXR _cell.length_a 80.72 _cell.length_b 80.72 _cell.length_c 504.77 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6TXR _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall 'P 4abw 2nw' _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB,NB,OB,PB,QB,RB,SB,TB,UB,VB,WB,XB,YB,ZB,AC,BC,CC,DC,EC,FC _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 ? 6 L N N ? 6 M N N ? 6 N N N ? 6 Q N N ? 6 R N N ? 6 X N N ? 6 Z N N ? 6 IA N N ? 6 JA N N ? 6 KA N N ? 6 WA N N ? 6 XA N N ? 6 YA N N ? 6 BB N N ? 6 CB N N ? 6 IB N N ? 6 KB N N ? 6 UB N N ? 6 VB N N ? 6 WB 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 E CAS O0Q . A O0Q 401 1_555 O C5 DU . A DU 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 F CAS O0Q . A O0Q 402 1_555 I C5 DU . A DU 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.532 ? covale ? covale3 DA CAS O0Q . B O0Q 401 1_555 GA C5 DU . B DU 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.155 ? covale ? covale4 EA CAS O0Q . B O0Q 402 1_555 PA C5 DU . B DU 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.241 ? covale ? covale5 QA CAS O0Q . C O0Q 401 1_555 ZA C5 DU . C DU 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.507 ? covale ? covale6 RA CAS O0Q . C O0Q 402 1_555 UA C5 DU . C DU 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.118 ? covale ? covale7 OB CAS O0Q . D O0Q 401 1_555 BC C5 DU . D DU 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.55 ? covale ? covale8 PB CAS O0Q . D O0Q 402 1_555 RB C5 DU . D DU 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.507 ? # _chem_comp.formula 'C9 H14 N3 O7 P' _chem_comp.formula_weight 307.197 _chem_comp.id DC _chem_comp.mon_nstd_flag y _chem_comp.name "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" _chem_comp.type 'dna 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 OP3 P DC sing 121 n n OP3 HOP3 DC sing 122 n n P OP1 DC doub 123 n n P OP2 DC sing 124 n n P O5' DC sing 125 n n OP2 HOP2 DC sing 126 n n O5' C5' DC sing 127 n n C5' C4' DC sing 128 n n C5' H5' DC sing 129 n n C5' "H5''" DC sing 130 n n C4' O4' DC sing 131 n n C4' C3' DC sing 132 n n C4' H4' DC sing 133 n n O4' C1' DC sing 134 n n C3' O3' DC sing 135 n n C3' C2' DC sing 136 n n C3' H3' DC sing 137 n n O3' HO3' DC sing 138 n n C2' C1' DC sing 139 n n C2' H2' DC sing 140 n n C2' "H2''" DC sing 141 n n C1' N1 DC sing 142 n n C1' H1' DC sing 143 n n N1 C2 DC sing 144 n n N1 C6 DC sing 145 n n C2 O2 DC doub 146 n n C2 N3 DC sing 147 n n N3 C4 DC doub 148 n n C4 N4 DC sing 149 n n C4 C5 DC sing 150 n n N4 H41 DC sing 151 n n N4 H42 DC sing 152 n n C5 C6 DC doub 153 n n C5 H5 DC sing 154 n n C6 H6 DC sing 155 n n # _atom_sites.entry_id 6TXR _atom_sites.fract_transf_matrix[1][1] 0.012389 _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] 0.012389 _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] 0.001981 _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 2 O0Q A 1 401 2 O0Q DRG . F 2 O0Q A 1 402 3 O0Q DRG . G 3 DG A 1 403 1 DG Gd . H 3 DG A 1 404 2 DG Gd . I 4 DU A 1 405 3 DU Td . J 3 DG A 1 406 7 DG Gd . K 5 DA A 1 407 8 DA Ad . L 6 DC A 1 408 9 DC Cd . M 6 DC A 1 409 18 DC Cd . N 6 DC A 1 410 19 DC Cd . O 4 DU A 1 411 20 DU Td . P 5 DA A 1 412 21 DA Ad . Q 6 DC A 1 413 22 DC Cd . R 6 DC A 1 414 23 DC Cd . S 3 DG A 1 415 24 DG Gd . T 5 DA A 1 416 25 DA Ad . U 3 DG A 1 417 26 DG Gd . V 3 DG A 1 418 27 DG Gd . W 3 DG A 1 419 28 DG Gd . X 6 DC A 1 420 29 DC Cd . Y 5 DA A 1 421 30 DA Ad . Z 6 DC A 1 422 31 DC Cd . AA 3 DG A 1 423 32 DG Gd . BA 3 DG A 1 424 33 DG Gd . CA 5 DA A 1 425 34 DA Ad . DA 2 O0Q B 1 401 1 O0Q DRG . EA 2 O0Q B 1 402 9 O0Q DRG . FA 5 DA B 1 403 4 DA Ad . GA 4 DU B 1 404 5 DU Td . HA 5 DA B 1 405 6 DA Ad . IA 6 DC B 1 406 10 DC Cd . JA 6 DC B 1 407 11 DC Cd . KA 6 DC B 1 408 12 DC Cd . LA 4 DU B 1 409 13 DU Td . MA 3 DG B 1 410 14 DG Gd . NA 5 DA B 1 411 15 DA Ad . OA 3 DG B 1 412 16 DG Gd . PA 4 DU B 1 413 17 DU Td . QA 2 O0Q C 1 401 6 O0Q DRG . RA 2 O0Q C 1 402 7 O0Q DRG . SA 3 DG C 1 403 1 DG Gd . TA 3 DG C 1 404 2 DG Gd . UA 4 DU C 1 405 3 DU Td . VA 5 DA C 1 406 8 DA Ad . WA 6 DC C 1 407 9 DC Cd . XA 6 DC C 1 408 18 DC Cd . YA 6 DC C 1 409 19 DC Cd . ZA 4 DU C 1 410 20 DU Td . AB 5 DA C 1 411 21 DA Ad . BB 6 DC C 1 412 22 DC Cd . CB 6 DC C 1 413 23 DC Cd . DB 3 DG C 1 414 24 DG Gd . EB 5 DA C 1 415 25 DA Ad . FB 3 DG C 1 416 26 DG Gd . GB 3 DG C 1 417 27 DG Gd . HB 3 DG C 1 418 28 DG Gd . IB 6 DC C 1 419 29 DC Cd . JB 5 DA C 1 420 30 DA Ad . KB 6 DC C 1 421 31 DC Cd . LB 3 DG C 1 422 32 DG Gd . MB 3 DG C 1 423 33 DG Gd . NB 5 DA C 1 424 34 DA Ad . OB 2 O0Q D 1 401 8 O0Q DRG . PB 2 O0Q D 1 402 10 O0Q DRG . QB 5 DA D 1 403 4 DA Ad . RB 4 DU D 1 404 5 DU Td . SB 5 DA D 1 405 6 DA Ad . TB 3 DG D 1 406 7 DG Gd . UB 6 DC D 1 407 10 DC Cd . VB 6 DC D 1 408 11 DC Cd . WB 6 DC D 1 409 12 DC Cd . XB 4 DU D 1 410 13 DU Td . YB 3 DG D 1 411 14 DG Gd . ZB 5 DA D 1 412 15 DA Ad . AC 3 DG D 1 413 16 DG Gd . BC 4 DU D 1 414 17 DU Td . CC 7 HOH A 1 501 80 HOH HOH . CC 7 HOH A 2 502 59 HOH HOH . CC 7 HOH A 3 503 99 HOH HOH . CC 7 HOH A 4 504 20 HOH HOH . CC 7 HOH A 5 505 83 HOH HOH . CC 7 HOH A 6 506 49 HOH HOH . CC 7 HOH A 7 507 3 HOH HOH . CC 7 HOH A 8 508 92 HOH HOH . CC 7 HOH A 9 509 77 HOH HOH . CC 7 HOH A 10 510 72 HOH HOH . CC 7 HOH A 11 511 7 HOH HOH . CC 7 HOH A 12 512 13 HOH HOH . CC 7 HOH A 13 513 38 HOH HOH . CC 7 HOH A 14 514 75 HOH HOH . CC 7 HOH A 15 515 71 HOH HOH . CC 7 HOH A 16 516 40 HOH HOH . CC 7 HOH A 17 517 43 HOH HOH . CC 7 HOH A 18 518 73 HOH HOH . CC 7 HOH A 19 519 82 HOH HOH . CC 7 HOH A 20 520 74 HOH HOH . CC 7 HOH A 21 521 58 HOH HOH . CC 7 HOH A 22 522 19 HOH HOH . CC 7 HOH A 23 523 104 HOH HOH . CC 7 HOH A 24 524 78 HOH HOH . CC 7 HOH A 25 525 98 HOH HOH . DC 7 HOH B 1 501 94 HOH HOH . DC 7 HOH B 2 502 53 HOH HOH . DC 7 HOH B 3 503 61 HOH HOH . DC 7 HOH B 4 504 29 HOH HOH . DC 7 HOH B 5 505 18 HOH HOH . DC 7 HOH B 6 506 25 HOH HOH . DC 7 HOH B 7 507 2 HOH HOH . DC 7 HOH B 8 508 1 HOH HOH . DC 7 HOH B 9 509 50 HOH HOH . DC 7 HOH B 10 510 35 HOH HOH . DC 7 HOH B 11 511 54 HOH HOH . DC 7 HOH B 12 512 24 HOH HOH . DC 7 HOH B 13 513 87 HOH HOH . DC 7 HOH B 14 514 23 HOH HOH . DC 7 HOH B 15 515 39 HOH HOH . DC 7 HOH B 16 516 45 HOH HOH . DC 7 HOH B 17 517 91 HOH HOH . DC 7 HOH B 18 518 62 HOH HOH . DC 7 HOH B 19 519 101 HOH HOH . DC 7 HOH B 20 520 9 HOH HOH . DC 7 HOH B 21 521 56 HOH HOH . DC 7 HOH B 22 522 11 HOH HOH . DC 7 HOH B 23 523 42 HOH HOH . DC 7 HOH B 24 524 102 HOH HOH . DC 7 HOH B 25 525 15 HOH HOH . DC 7 HOH B 26 526 68 HOH HOH . DC 7 HOH B 27 527 93 HOH HOH . DC 7 HOH B 28 528 88 HOH HOH . EC 7 HOH C 1 501 55 HOH HOH . EC 7 HOH C 2 502 6 HOH HOH . EC 7 HOH C 3 503 86 HOH HOH . EC 7 HOH C 4 504 85 HOH HOH . EC 7 HOH C 5 505 90 HOH HOH . EC 7 HOH C 6 506 31 HOH HOH . EC 7 HOH C 7 507 5 HOH HOH . EC 7 HOH C 8 508 28 HOH HOH . EC 7 HOH C 9 509 67 HOH HOH . EC 7 HOH C 10 510 30 HOH HOH . EC 7 HOH C 11 511 81 HOH HOH . EC 7 HOH C 12 512 63 HOH HOH . EC 7 HOH C 13 513 79 HOH HOH . EC 7 HOH C 14 514 97 HOH HOH . EC 7 HOH C 15 515 41 HOH HOH . EC 7 HOH C 16 516 69 HOH HOH . EC 7 HOH C 17 517 34 HOH HOH . EC 7 HOH C 18 518 16 HOH HOH . EC 7 HOH C 19 519 60 HOH HOH . EC 7 HOH C 20 520 96 HOH HOH . EC 7 HOH C 21 521 89 HOH HOH . FC 7 HOH D 1 501 27 HOH HOH . FC 7 HOH D 2 502 37 HOH HOH . FC 7 HOH D 3 503 14 HOH HOH . FC 7 HOH D 4 504 32 HOH HOH . FC 7 HOH D 5 505 17 HOH HOH . FC 7 HOH D 6 506 70 HOH HOH . FC 7 HOH D 7 507 21 HOH HOH . FC 7 HOH D 8 508 95 HOH HOH . FC 7 HOH D 9 509 33 HOH HOH . FC 7 HOH D 10 510 46 HOH HOH . FC 7 HOH D 11 511 65 HOH HOH . FC 7 HOH D 12 512 36 HOH HOH . FC 7 HOH D 13 513 22 HOH HOH . FC 7 HOH D 14 514 44 HOH HOH . FC 7 HOH D 15 515 8 HOH HOH . FC 7 HOH D 16 516 10 HOH HOH . FC 7 HOH D 17 517 12 HOH HOH . FC 7 HOH D 18 518 64 HOH HOH . FC 7 HOH D 19 519 4 HOH HOH . FC 7 HOH D 20 520 76 HOH HOH . FC 7 HOH D 21 521 57 HOH HOH . FC 7 HOH D 22 522 26 HOH HOH . FC 7 HOH D 23 523 47 HOH HOH . FC 7 HOH D 24 524 100 HOH HOH . FC 7 HOH D 25 525 52 HOH HOH . FC 7 HOH D 26 526 51 HOH HOH . FC 7 HOH D 27 527 48 HOH HOH . FC 7 HOH D 28 528 66 HOH HOH . FC 7 HOH D 29 529 84 HOH HOH . FC 7 HOH D 30 530 103 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 DC . . . IA 6 -23.845 48.899 -3.975 1 81.7 ? P DC 406 B 1 HETATM 2 O OP1 DC . . . IA 6 -23.245 49.488 -5.194 1 88.73 ? OP1 DC 406 B 1 HETATM 3 O OP2 DC . . . IA 6 -24.14 49.732 -2.784 1 74.25 -1 OP2 DC 406 B 1 HETATM 4 O O5' DC . . . IA 6 -25.163 48.147 -4.424 1 69.3 ? O5' DC 406 B 1 HETATM 5 C C5' DC . . . IA 6 -25.81 48.523 -5.569 1 74.12 ? C5' DC 406 B 1 HETATM 6 C C4' DC . . . IA 6 -26.78 47.439 -5.972 1 86.3 ? C4' DC 406 B 1 HETATM 7 O O4' DC . . . IA 6 -26.737 46.353 -4.994 1 85.55 ? O4' DC 406 B 1 HETATM 8 C C3' DC . . . IA 6 -28.216 47.9 -5.99 1 92.96 ? C3' DC 406 B 1 HETATM 9 O O3' DC . . . IA 6 -28.989 47.129 -6.902 1 98.46 ? O3' DC 406 B 1 HETATM 10 C C2' DC . . . IA 6 -28.636 47.651 -4.541 1 87.71 ? C2' DC 406 B 1 HETATM 11 C C1' DC . . . IA 6 -27.957 46.321 -4.265 1 84.49 ? C1' DC 406 B 1 HETATM 12 N N1 DC . . . IA 6 -27.666 46.105 -2.828 1 80.81 ? N1 DC 406 B 1 HETATM 13 C C2 DC . . . IA 6 -28.041 44.895 -2.197 1 78.21 ? C2 DC 406 B 1 HETATM 14 O O2 DC . . . IA 6 -28.607 44.02 -2.857 1 80.6 ? O2 DC 406 B 1 HETATM 15 N N3 DC . . . IA 6 -27.762 44.725 -0.874 1 73.44 ? N3 DC 406 B 1 HETATM 16 C C4 DC . . . IA 6 -27.157 45.707 -0.195 1 67.94 ? C4 DC 406 B 1 HETATM 17 N N4 DC . . . IA 6 -26.901 45.513 1.096 1 61.01 ? N4 DC 406 B 1 HETATM 18 C C5 DC . . . IA 6 -26.783 46.935 -0.819 1 69.03 ? C5 DC 406 B 1 HETATM 19 C C6 DC . . . IA 6 -27.066 47.093 -2.119 1 73.89 ? C6 DC 406 B 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 19 #