data_3C4V # _model_server_result.job_id hb8jxtV6l7BaqSXFZkoARw _model_server_result.datetime_utc '2024-11-13 08:59:39' _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 3c4v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":600}' # _entry.id 3C4V # _exptl.entry_id 3C4V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _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 3C4V _cell.length_a 223.94 _cell.length_b 223.94 _cell.length_c 125.005 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3C4V _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 2' # 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 PISA hexadecameric 16 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,H 1 1,2 B,E,F,G,I 2 1,3 A,B,C,D,E,F,G,H,I 3 1,4,5,6,3,7,2,8 # 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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 3 'crystal symmetry operation' 5_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 223.94 0 0 4 'crystal symmetry operation' 2_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 223.94 223.94 0 5 'crystal symmetry operation' 3_655 -y+1,x,z 0 -1 0 1 0 0 0 0 1 223.94 0 0 6 'crystal symmetry operation' 4_565 y,-x+1,z 0 1 0 -1 0 0 0 0 1 0 223.94 0 7 'crystal symmetry operation' 6_565 x,-y+1,-z 1 0 0 0 -1 0 0 0 -1 0 223.94 0 8 'crystal symmetry operation' 8_665 -y+1,-x+1,-z 0 -1 0 -1 0 0 0 0 -1 223.94 223.94 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F 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 O ALA 306 A ALA 306 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc2 A OG1 THR 330 A THR 330 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc3 C MG MG . A MG 602 1_555 H O HOH . A HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc4 B O ALA 306 B ALA 306 1_555 E MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? metalc ? metalc5 E MG MG . B MG 602 1_555 I O HOH . B HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna 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 N1 C2 UDP sing 385 n n N1 C6 UDP sing 386 n n N1 C1' UDP sing 387 n n C2 N3 UDP sing 388 n n C2 O2 UDP doub 389 n n N3 C4 UDP sing 390 n n N3 HN3 UDP sing 391 n n C4 C5 UDP sing 392 n n C4 O4 UDP doub 393 n n C5 C6 UDP doub 394 n n C5 H5 UDP sing 395 n n C6 H6 UDP sing 396 n n C1' C2' UDP sing 397 n n C1' O4' UDP sing 398 n n C1' H1' UDP sing 399 n n C2' O2' UDP sing 400 n n C2' C3' UDP sing 401 n n C2' H2' UDP sing 402 n n O2' HO2' UDP sing 403 n n C3' C4' UDP sing 404 n n C3' O3' UDP sing 405 n n C3' H3' UDP sing 406 n n C4' O4' UDP sing 407 n n C4' C5' UDP sing 408 n n C4' H4' UDP sing 409 n n O3' HO3' UDP sing 410 n n C5' O5' UDP sing 411 n n C5' "H5'1" UDP sing 412 n n C5' "H5'2" UDP sing 413 n n O5' PA UDP sing 414 n n PA O1A UDP doub 415 n n PA O2A UDP sing 416 n n PA O3A UDP sing 417 n n O2A HOA2 UDP sing 418 n n O3A PB UDP sing 419 n n PB O1B UDP doub 420 n n PB O2B UDP sing 421 n n PB O3B UDP sing 422 n n O2B HOB2 UDP sing 423 n n O3B HOB3 UDP sing 424 n n # _atom_sites.entry_id 3C4V _atom_sites.fract_transf_matrix[1][1] 0.004465 _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] 0.004465 _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] 0.008 _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 1 602 602 MG MG . D 3 UDP A 1 600 600 UDP UDP . E 2 MG B 1 602 602 MG MG . F 3 UDP B 1 600 600 UDP UDP . G 4 LIP B 1 601 601 LIP 1IP . H 5 HOH A 1 603 3 HOH HOH . H 5 HOH A 2 604 4 HOH HOH . H 5 HOH A 3 605 9 HOH HOH . H 5 HOH A 4 606 10 HOH HOH . H 5 HOH A 5 607 11 HOH HOH . H 5 HOH A 6 608 12 HOH HOH . H 5 HOH A 7 609 13 HOH HOH . H 5 HOH A 8 610 14 HOH HOH . H 5 HOH A 9 611 15 HOH HOH . H 5 HOH A 10 612 16 HOH HOH . H 5 HOH A 11 613 28 HOH HOH . H 5 HOH A 12 614 29 HOH HOH . H 5 HOH A 13 615 32 HOH HOH . H 5 HOH A 14 616 33 HOH HOH . H 5 HOH A 15 617 34 HOH HOH . H 5 HOH A 16 618 35 HOH HOH . H 5 HOH A 17 619 36 HOH HOH . H 5 HOH A 18 620 37 HOH HOH . H 5 HOH A 19 621 38 HOH HOH . H 5 HOH A 20 622 39 HOH HOH . H 5 HOH A 21 623 40 HOH HOH . H 5 HOH A 22 624 41 HOH HOH . H 5 HOH A 23 625 42 HOH HOH . H 5 HOH A 24 626 43 HOH HOH . H 5 HOH A 25 627 44 HOH HOH . H 5 HOH A 26 628 45 HOH HOH . H 5 HOH A 27 629 46 HOH HOH . H 5 HOH A 28 630 47 HOH HOH . H 5 HOH A 29 631 48 HOH HOH . H 5 HOH A 30 632 49 HOH HOH . H 5 HOH A 31 633 50 HOH HOH . H 5 HOH A 32 634 51 HOH HOH . H 5 HOH A 33 635 52 HOH HOH . H 5 HOH A 34 636 53 HOH HOH . H 5 HOH A 35 637 54 HOH HOH . H 5 HOH A 36 638 55 HOH HOH . H 5 HOH A 37 639 56 HOH HOH . H 5 HOH A 38 640 72 HOH HOH . I 5 HOH B 1 603 5 HOH HOH . I 5 HOH B 2 604 6 HOH HOH . I 5 HOH B 3 605 7 HOH HOH . I 5 HOH B 4 606 8 HOH HOH . I 5 HOH B 5 607 18 HOH HOH . I 5 HOH B 6 608 19 HOH HOH . I 5 HOH B 7 609 20 HOH HOH . I 5 HOH B 8 610 21 HOH HOH . I 5 HOH B 9 611 22 HOH HOH . I 5 HOH B 10 612 23 HOH HOH . I 5 HOH B 11 613 24 HOH HOH . I 5 HOH B 12 614 25 HOH HOH . I 5 HOH B 13 615 26 HOH HOH . I 5 HOH B 14 616 27 HOH HOH . I 5 HOH B 15 617 30 HOH HOH . I 5 HOH B 16 618 31 HOH HOH . I 5 HOH B 17 619 57 HOH HOH . I 5 HOH B 18 620 58 HOH HOH . I 5 HOH B 19 621 59 HOH HOH . I 5 HOH B 20 622 60 HOH HOH . I 5 HOH B 21 623 61 HOH HOH . I 5 HOH B 22 624 62 HOH HOH . I 5 HOH B 23 625 63 HOH HOH . I 5 HOH B 24 626 64 HOH HOH . I 5 HOH B 25 627 65 HOH HOH . I 5 HOH B 26 628 66 HOH HOH . I 5 HOH B 27 629 67 HOH HOH . I 5 HOH B 28 630 68 HOH HOH . I 5 HOH B 29 631 69 HOH HOH . I 5 HOH B 30 632 70 HOH HOH . I 5 HOH B 31 633 71 HOH HOH . I 5 HOH B 32 634 73 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 UDP . . . D 3 81.496 45.658 12.342 1 31.76 ? N1 UDP 600 A 1 HETATM 2 C C2 UDP . . . D 3 81.831 44.544 11.625 1 30.6 ? C2 UDP 600 A 1 HETATM 3 N N3 UDP . . . D 3 83.036 44.494 10.995 1 31.6 ? N3 UDP 600 A 1 HETATM 4 C C4 UDP . . . D 3 83.906 45.552 11.084 1 32.65 ? C4 UDP 600 A 1 HETATM 5 C C5 UDP . . . D 3 83.548 46.68 11.813 1 30.82 ? C5 UDP 600 A 1 HETATM 6 C C6 UDP . . . D 3 82.241 46.796 12.257 1 29.96 ? C6 UDP 600 A 1 HETATM 7 O O2 UDP . . . D 3 81.041 43.604 11.529 1 31.87 ? O2 UDP 600 A 1 HETATM 8 O O4 UDP . . . D 3 85.001 45.488 10.498 1 33.47 ? O4 UDP 600 A 1 HETATM 9 C C1' UDP . . . D 3 80.201 45.633 13.022 1 33.36 ? C1' UDP 600 A 1 HETATM 10 C C2' UDP . . . D 3 80.404 45.403 14.521 1 34.39 ? C2' UDP 600 A 1 HETATM 11 O O2' UDP . . . D 3 80.442 44.008 14.792 1 30.47 ? O2' UDP 600 A 1 HETATM 12 C C3' UDP . . . D 3 79.184 46.087 15.123 1 36.86 ? C3' UDP 600 A 1 HETATM 13 C C4' UDP . . . D 3 78.697 47.038 14.02 1 39.68 ? C4' UDP 600 A 1 HETATM 14 O O4' UDP . . . D 3 79.548 46.857 12.917 1 36.36 ? O4' UDP 600 A 1 HETATM 15 O O3' UDP . . . D 3 78.153 45.156 15.399 1 32.05 ? O3' UDP 600 A 1 HETATM 16 C C5' UDP . . . D 3 78.768 48.513 14.371 1 44.13 ? C5' UDP 600 A 1 HETATM 17 O O5' UDP . . . D 3 78.071 48.643 15.595 1 53.78 ? O5' UDP 600 A 1 HETATM 18 P PA UDP . . . D 3 77.852 50.131 16.239 1 57.05 ? PA UDP 600 A 1 HETATM 19 O O1A UDP . . . D 3 76.836 50.042 17.338 1 54.49 ? O1A UDP 600 A 1 HETATM 20 O O2A UDP . . . D 3 79.118 50.8 16.73 1 55.87 ? O2A UDP 600 A 1 HETATM 21 O O3A UDP . . . D 3 77.388 50.861 14.867 1 55.38 ? O3A UDP 600 A 1 HETATM 22 P PB UDP . . . D 3 76.103 51.768 14.955 1 50 ? PB UDP 600 A 1 HETATM 23 O O1B UDP . . . D 3 76.571 53.157 15.002 1 48.78 ? O1B UDP 600 A 1 HETATM 24 O O2B UDP . . . D 3 75.243 51.461 16.092 1 54.81 ? O2B UDP 600 A 1 HETATM 25 O O3B UDP . . . D 3 75.284 51.395 13.793 1 55.69 ? O3B UDP 600 A 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 248 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 25 #