data_6TXR # _model_server_result.job_id T-2zL2EfKfeNIAT-778pWg _model_server_result.datetime_utc '2024-11-25 14:00:47' _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":"GA","auth_seq_id":404}' # _entry.id 6TXR # _exptl.entry_id 6TXR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 10 _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 ? 4 I N N ? 4 O N N ? 4 GA N N ? 4 LA N N ? 4 PA N N ? 4 UA N N ? 4 ZA N N ? 4 RB N N ? 4 XB N N ? 4 BC 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 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id DU _chem_comp.mon_nstd_flag y _chem_comp.name "2'-DEOXYURIDINE-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 DU sing 195 n n OP3 HOP3 DU sing 196 n n P OP1 DU doub 197 n n P OP2 DU sing 198 n n P O5' DU sing 199 n n OP2 HOP2 DU sing 200 n n O5' C5' DU sing 201 n n C5' C4' DU sing 202 n n C5' H5' DU sing 203 n n C5' "H5''" DU sing 204 n n C4' O4' DU sing 205 n n C4' C3' DU sing 206 n n C4' H4' DU sing 207 n n O4' C1' DU sing 208 n n C3' O3' DU sing 209 n n C3' C2' DU sing 210 n n C3' H3' DU sing 211 n n O3' HO3' DU sing 212 n n C2' C1' DU sing 213 n n C2' H2' DU sing 214 n n C2' "H2''" DU sing 215 n n C1' N1 DU sing 216 n n C1' H1' DU sing 217 n n N1 C2 DU sing 218 n n N1 C6 DU sing 219 n n C2 O2 DU doub 220 n n C2 N3 DU sing 221 n n N3 C4 DU sing 222 n n N3 H3 DU sing 223 n n C4 O4 DU doub 224 n n C4 C5 DU sing 225 n n C5 C6 DU doub 226 n n C5 H5 DU sing 227 n n C6 H6 DU sing 228 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 DU . . . GA 4 -16.477 26.641 3.411 1 72.2 ? P DU 404 B 1 HETATM 2 O OP1 DU . . . GA 4 -15.433 26.211 2.461 1 80.47 -1 OP1 DU 404 B 1 HETATM 3 O OP2 DU . . . GA 4 -17.666 25.803 3.653 1 77.6 ? OP2 DU 404 B 1 HETATM 4 O O5' DU . . . GA 4 -17.024 28.032 2.913 1 70.74 ? O5' DU 404 B 1 HETATM 5 C C5' DU . . . GA 4 -17.38 29.02 3.84 1 68.71 ? C5' DU 404 B 1 HETATM 6 C C4' DU . . . GA 4 -17.716 30.271 3.088 1 76.33 ? C4' DU 404 B 1 HETATM 7 O O4' DU . . . GA 4 -16.539 31.091 3.043 1 80.78 ? O4' DU 404 B 1 HETATM 8 C C3' DU . . . GA 4 -18.085 29.992 1.647 1 76.48 ? C3' DU 404 B 1 HETATM 9 O O3' DU . . . GA 4 -19.563 29.924 1.47 1 83.87 ? O3' DU 404 B 1 HETATM 10 C C2' DU . . . GA 4 -17.358 31.053 0.807 1 71.99 ? C2' DU 404 B 1 HETATM 11 C C1' DU . . . GA 4 -16.432 31.751 1.806 1 70.77 ? C1' DU 404 B 1 HETATM 12 N N1 DU . . . GA 4 -14.942 31.833 1.461 1 62.72 ? N1 DU 404 B 1 HETATM 13 C C2 DU . . . GA 4 -14.376 33.091 1.29 1 64.84 ? C2 DU 404 B 1 HETATM 14 O O2 DU . . . GA 4 -15.026 34.126 1.341 1 67.19 ? O2 DU 404 B 1 HETATM 15 N N3 DU . . . GA 4 -13.021 33.098 1.05 1 59.07 ? N3 DU 404 B 1 HETATM 16 C C4 DU . . . GA 4 -12.174 32.009 0.988 1 62.69 ? C4 DU 404 B 1 HETATM 17 O O4 DU . . . GA 4 -10.968 32.142 0.767 1 55.81 ? O4 DU 404 B 1 HETATM 18 C C5 DU . . . GA 4 -12.825 30.707 1.194 1 62.88 ? C5 DU 404 B 1 HETATM 19 C C6 DU . . . GA 4 -14.158 30.683 1.437 1 59.9 ? C6 DU 404 B 1 # _model_server_stats.io_time_ms 203 _model_server_stats.parse_time_ms 152 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 19 #