data_3C4V # _model_server_result.job_id 1Fo3aoks5ujeMQkw3lnpoA _model_server_result.datetime_utc '2024-11-13 09:05:23' _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":"F","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 . . . F 3 86.656 43.382 -12.574 1 27.55 ? N1 UDP 600 B 1 HETATM 2 C C2 UDP . . . F 3 85.658 42.818 -11.839 1 25.02 ? C2 UDP 600 B 1 HETATM 3 N N3 UDP . . . F 3 84.725 43.637 -11.228 1 24.42 ? N3 UDP 600 B 1 HETATM 4 C C4 UDP . . . F 3 84.81 45.012 -11.382 1 26.72 ? C4 UDP 600 B 1 HETATM 5 C C5 UDP . . . F 3 85.834 45.543 -12.143 1 25.84 ? C5 UDP 600 B 1 HETATM 6 C C6 UDP . . . F 3 86.91 44.715 -12.452 1 26.15 ? C6 UDP 600 B 1 HETATM 7 O O2 UDP . . . F 3 85.644 41.573 -11.742 1 25.73 ? O2 UDP 600 B 1 HETATM 8 O O4 UDP . . . F 3 83.984 45.785 -10.853 1 27.16 ? O4 UDP 600 B 1 HETATM 9 C C1' UDP . . . F 3 87.607 42.491 -13.242 1 30.97 ? C1' UDP 600 B 1 HETATM 10 C C2' UDP . . . F 3 87.257 42.471 -14.746 1 33.58 ? C2' UDP 600 B 1 HETATM 11 O O2' UDP . . . F 3 86.337 41.447 -15.063 1 31.46 ? O2' UDP 600 B 1 HETATM 12 C C3' UDP . . . F 3 88.597 42.166 -15.383 1 35.04 ? C3' UDP 600 B 1 HETATM 13 C C4' UDP . . . F 3 89.635 42.496 -14.326 1 37.47 ? C4' UDP 600 B 1 HETATM 14 O O4' UDP . . . F 3 88.919 43.033 -13.228 1 35.89 ? O4' UDP 600 B 1 HETATM 15 O O3' UDP . . . F 3 88.718 40.779 -15.462 1 30.98 ? O3' UDP 600 B 1 HETATM 16 C C5' UDP . . . F 3 90.673 43.476 -14.849 1 42.42 ? C5' UDP 600 B 1 HETATM 17 O O5' UDP . . . F 3 91.337 42.874 -15.975 1 48.12 ? O5' UDP 600 B 1 HETATM 18 P PA UDP . . . F 3 92.48 43.734 -16.785 1 48.82 ? PA UDP 600 B 1 HETATM 19 O O1A UDP . . . F 3 93.436 42.83 -17.535 1 48.31 ? O1A UDP 600 B 1 HETATM 20 O O2A UDP . . . F 3 91.876 44.826 -17.638 1 47.49 ? O2A UDP 600 B 1 HETATM 21 O O3A UDP . . . F 3 93.11 44.467 -15.478 1 49.49 ? O3A UDP 600 B 1 HETATM 22 P PB UDP . . . F 3 94.619 44.168 -15.087 1 45.51 ? PB UDP 600 B 1 HETATM 23 O O1B UDP . . . F 3 95.38 45.351 -15.56 1 44.13 ? O1B UDP 600 B 1 HETATM 24 O O2B UDP . . . F 3 94.585 44.083 -13.595 1 50.9 ? O2B UDP 600 B 1 HETATM 25 O O3B UDP . . . F 3 95.138 42.878 -15.588 1 45.3 ? O3B UDP 600 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 25 #