data_4WTA
#
_model_server_result.job_id            oGDLYKOa1zvaV3iQLK_DTw 
_model_server_result.datetime_utc      '2024-11-22 11:33:43' 
_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          4wta 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":605}' 
#
_entry.id    4WTA 
#
_exptl.entry_id    4WTA 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_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         120 
_cell.entry_id            4WTA 
_cell.length_a            140.62 
_cell.length_b            140.62 
_cell.length_c            91 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4WTA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        170 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      5 
_struct_asym.id                             H 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 B O3' U 8 P U 6 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? 
metalc ? metalc2 J O HOH . P HOH 101 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? 
metalc ? metalc3 C OD1 ASP 222 A ASP 220 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
metalc ? metalc4 C OD2 ASP 222 A ASP 220 1_555 E MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc5 C O THR 223 A THR 221 1_555 E MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? 
metalc ? metalc6 C OE2 GLU 239 A GLU 237 1_555 F MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.828 ? 
metalc ? metalc7 C ND1 HIS 256 A HIS 254 1_555 F MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? 
metalc ? metalc8 C OD1 ASP 320 A ASP 318 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? 
metalc ? metalc9 C OD2 ASP 320 A ASP 318 1_555 E MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
metalc ? metalc10 C OD1 ASP 321 A ASP 319 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? 
metalc ? metalc11 D MN MN . A MN 601 1_555 H O1A UDP . A UDP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? 
metalc ? metalc12 E MN MN . A MN 602 1_555 H O1B UDP . A UDP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? 
metalc ? metalc13 E MN MN . A MN 602 1_555 H O1A UDP . A UDP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.936 ? 
metalc ? metalc14 E MN MN . A MN 602 1_555 K O HOH . A HOH 716 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? 
hydrog WATSON-CRICK hydrog1 A N1 A 3 T A 3 1_555 B N3 U 8 P U 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A N6 A 3 T A 3 1_555 B O4 U 8 P U 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A N1 A 4 T A 4 1_555 B N3 U 7 P U 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 A N6 A 4 T A 4 1_555 B O4 U 7 P U 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 A N1 A 5 T A 5 1_555 B N3 U 6 P U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 A N6 A 5 T A 5 1_555 B O4 U 6 P U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 A N3 U 6 T U 6 1_555 B N1 A 5 P A 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 A O4 U 6 T U 6 1_555 B N6 A 5 P A 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 A N3 U 7 T U 7 1_555 B N1 A 4 P A 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 A O4 U 7 T U 7 1_555 B N6 A 4 P A 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_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 468 n n 
N1 C6 UDP sing 469 n n 
N1 C1' UDP sing 470 n n 
C2 N3 UDP sing 471 n n 
C2 O2 UDP doub 472 n n 
N3 C4 UDP sing 473 n n 
N3 HN3 UDP sing 474 n n 
C4 C5 UDP sing 475 n n 
C4 O4 UDP doub 476 n n 
C5 C6 UDP doub 477 n n 
C5 H5 UDP sing 478 n n 
C6 H6 UDP sing 479 n n 
C1' C2' UDP sing 480 n n 
C1' O4' UDP sing 481 n n 
C1' H1' UDP sing 482 n n 
C2' O2' UDP sing 483 n n 
C2' C3' UDP sing 484 n n 
C2' H2' UDP sing 485 n n 
O2' HO2' UDP sing 486 n n 
C3' C4' UDP sing 487 n n 
C3' O3' UDP sing 488 n n 
C3' H3' UDP sing 489 n n 
C4' O4' UDP sing 490 n n 
C4' C5' UDP sing 491 n n 
C4' H4' UDP sing 492 n n 
O3' HO3' UDP sing 493 n n 
C5' O5' UDP sing 494 n n 
C5' "H5'1" UDP sing 495 n n 
C5' "H5'2" UDP sing 496 n n 
O5' PA UDP sing 497 n n 
PA O1A UDP doub 498 n n 
PA O2A UDP sing 499 n n 
PA O3A UDP sing 500 n n 
O2A HOA2 UDP sing 501 n n 
O3A PB UDP sing 502 n n 
PB O1B UDP doub 503 n n 
PB O2B UDP sing 504 n n 
PB O3B UDP sing 505 n n 
O2B HOB2 UDP sing 506 n n 
O3B HOB3 UDP sing 507 n n 
#
_atom_sites.entry_id                     4WTA 
_atom_sites.fract_transf_matrix[1][1]    0.007111 
_atom_sites.fract_transf_matrix[1][2]    0.004106 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008211 
_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]    0.010989 
_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
D 3 MN A 1 601 1 MN MN . 
E 3 MN A 1 602 2 MN MN . 
F 3 MN A 1 603 3 MN MN . 
G 4 CL A 1 604 1 CL CL . 
H 5 UDP A 1 605 1 UDP UDP . 
I 6 HOH T 1 101 29 HOH HOH . 
J 6 HOH P 1 101 5 HOH HOH . 
J 6 HOH P 2 102 55 HOH HOH . 
J 6 HOH P 3 103 66 HOH HOH . 
K 6 HOH A 1 701 32 HOH HOH . 
K 6 HOH A 2 702 11 HOH HOH . 
K 6 HOH A 3 703 56 HOH HOH . 
K 6 HOH A 4 704 10 HOH HOH . 
K 6 HOH A 5 705 17 HOH HOH . 
K 6 HOH A 6 706 15 HOH HOH . 
K 6 HOH A 7 707 16 HOH HOH . 
K 6 HOH A 8 708 3 HOH HOH . 
K 6 HOH A 9 709 13 HOH HOH . 
K 6 HOH A 10 710 43 HOH HOH . 
K 6 HOH A 11 711 61 HOH HOH . 
K 6 HOH A 12 712 12 HOH HOH . 
K 6 HOH A 13 713 1 HOH HOH . 
K 6 HOH A 14 714 2 HOH HOH . 
K 6 HOH A 15 715 4 HOH HOH . 
K 6 HOH A 16 716 6 HOH HOH . 
K 6 HOH A 17 717 7 HOH HOH . 
K 6 HOH A 18 718 8 HOH HOH . 
K 6 HOH A 19 719 9 HOH HOH . 
K 6 HOH A 20 720 14 HOH HOH . 
K 6 HOH A 21 721 18 HOH HOH . 
K 6 HOH A 22 722 19 HOH HOH . 
K 6 HOH A 23 723 20 HOH HOH . 
K 6 HOH A 24 724 21 HOH HOH . 
K 6 HOH A 25 725 22 HOH HOH . 
K 6 HOH A 26 726 23 HOH HOH . 
K 6 HOH A 27 727 24 HOH HOH . 
K 6 HOH A 28 728 25 HOH HOH . 
K 6 HOH A 29 729 26 HOH HOH . 
K 6 HOH A 30 730 27 HOH HOH . 
K 6 HOH A 31 731 28 HOH HOH . 
K 6 HOH A 32 732 30 HOH HOH . 
K 6 HOH A 33 733 31 HOH HOH . 
K 6 HOH A 34 734 33 HOH HOH . 
K 6 HOH A 35 735 34 HOH HOH . 
K 6 HOH A 36 736 35 HOH HOH . 
K 6 HOH A 37 737 36 HOH HOH . 
K 6 HOH A 38 738 37 HOH HOH . 
K 6 HOH A 39 739 38 HOH HOH . 
K 6 HOH A 40 740 39 HOH HOH . 
K 6 HOH A 41 741 40 HOH HOH . 
K 6 HOH A 42 742 41 HOH HOH . 
K 6 HOH A 43 743 42 HOH HOH . 
K 6 HOH A 44 744 44 HOH HOH . 
K 6 HOH A 45 745 45 HOH HOH . 
K 6 HOH A 46 746 46 HOH HOH . 
K 6 HOH A 47 747 47 HOH HOH . 
K 6 HOH A 48 748 48 HOH HOH . 
K 6 HOH A 49 749 49 HOH HOH . 
K 6 HOH A 50 750 50 HOH HOH . 
K 6 HOH A 51 751 51 HOH HOH . 
K 6 HOH A 52 752 52 HOH HOH . 
K 6 HOH A 53 753 53 HOH HOH . 
K 6 HOH A 54 754 54 HOH HOH . 
K 6 HOH A 55 755 57 HOH HOH . 
K 6 HOH A 56 756 58 HOH HOH . 
K 6 HOH A 57 757 59 HOH HOH . 
K 6 HOH A 58 758 60 HOH HOH . 
K 6 HOH A 59 759 62 HOH HOH . 
K 6 HOH A 60 760 63 HOH HOH . 
K 6 HOH A 61 761 64 HOH HOH . 
K 6 HOH A 62 762 65 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 . . . H 5 40.002 -46.115 7.263 1 47.57 ? N1 UDP 605 A 1 
HETATM 2 C C2 UDP . . . H 5 39.173 -46.039 8.417 1 51.69 ? C2 UDP 605 A 1 
HETATM 3 N N3 UDP . . . H 5 39.629 -45.544 9.564 1 54.88 ? N3 UDP 605 A 1 
HETATM 4 C C4 UDP . . . H 5 40.888 -45.085 9.648 1 55.13 ? C4 UDP 605 A 1 
HETATM 5 C C5 UDP . . . H 5 41.738 -45.129 8.527 1 52.66 ? C5 UDP 605 A 1 
HETATM 6 C C6 UDP . . . H 5 41.259 -45.645 7.318 1 49.39 ? C6 UDP 605 A 1 
HETATM 7 O O2 UDP . . . H 5 38 -46.445 8.405 1 52.1 ? O2 UDP 605 A 1 
HETATM 8 O O4 UDP . . . H 5 41.272 -44.619 10.749 1 52.03 ? O4 UDP 605 A 1 
HETATM 9 C C1' UDP . . . H 5 39.431 -46.636 6.029 1 44.37 ? C1' UDP 605 A 1 
HETATM 10 C C2' UDP . . . H 5 38.806 -45.435 5.333 1 45.63 ? C2' UDP 605 A 1 
HETATM 11 O O2' UDP . . . H 5 37.553 -45.77 4.706 1 47.33 ? O2' UDP 605 A 1 
HETATM 12 C C3' UDP . . . H 5 39.863 -45.041 4.334 1 44.63 ? C3' UDP 605 A 1 
HETATM 13 C C4' UDP . . . H 5 40.418 -46.387 3.928 1 45.13 ? C4' UDP 605 A 1 
HETATM 14 O O4' UDP . . . H 5 40.4 -47.151 5.14 1 43.98 ? O4' UDP 605 A 1 
HETATM 15 O O3' UDP . . . H 5 39.326 -44.289 3.247 1 47.14 ? O3' UDP 605 A 1 
HETATM 16 C C5' UDP . . . H 5 41.812 -46.341 3.293 1 46.52 ? C5' UDP 605 A 1 
HETATM 17 O O5' UDP . . . H 5 42.773 -45.795 4.216 1 48.72 ? O5' UDP 605 A 1 
HETATM 18 P PA UDP . . . H 5 43.992 -44.854 3.765 1 43.72 ? PA UDP 605 A 1 
HETATM 19 O O1A UDP . . . H 5 44.435 -45.269 2.38 1 45.24 ? O1A UDP 605 A 1 
HETATM 20 O O2A UDP . . . H 5 44.941 -45.019 4.903 1 47.87 ? O2A UDP 605 A 1 
HETATM 21 O O3A UDP . . . H 5 43.319 -43.382 3.749 1 40.22 ? O3A UDP 605 A 1 
HETATM 22 P PB UDP . . . H 5 42.473 -42.756 2.49 1 43.84 ? PB UDP 605 A 1 
HETATM 23 O O1B UDP . . . H 5 42.651 -43.71 1.325 1 32.28 ? O1B UDP 605 A 1 
HETATM 24 O O2B UDP . . . H 5 43.001 -41.316 2.394 1 40 ? O2B UDP 605 A 1 
HETATM 25 O O3B UDP . . . H 5 41.016 -42.658 2.911 1 42.14 ? O3B UDP 605 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           246 
_model_server_stats.encode_time_ms          19 
_model_server_stats.element_count           25 
#