data_1DDR
#
_model_server_result.job_id            ieCnEiEFvbB-V24ARPy9XQ 
_model_server_result.datetime_utc      '2024-11-06 02:58:04' 
_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          1ddr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":211}' 
#
_entry.id    1DDR 
#
_exptl.entry_id    1DDR 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              60.055 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            UREA 
_entity.pdbx_number_of_molecules    5 
_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            1DDR 
_cell.length_a            93.181 
_cell.length_b            93.185 
_cell.length_c            73.886 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1DDR 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        169 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 61' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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 E N N 
? 4 F N N 
? 4 G N N 
? 4 K N N 
? 4 L 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 OD1 ASN 18 A ASN 18 2_665 I CA CA . B CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? 
metalc ? metalc2 B O SER 135 B SER 135 1_555 I CA CA . B CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.098 ? 
metalc ? metalc3 B O ALA 143 B ALA 143 2_665 I CA CA . B CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? 
metalc ? metalc4 I CA CA . B CA 203 1_555 N O HOH . B HOH 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? 
#
_chem_comp.formula           'C H4 N2 O' 
_chem_comp.formula_weight    60.055 
_chem_comp.id                URE 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              UREA 
_chem_comp.type              non-polymer 
_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
C O URE doub 415 n n 
C N1 URE sing 416 n n 
C N2 URE sing 417 n n 
N1 HN11 URE sing 418 n n 
N1 HN12 URE sing 419 n n 
N2 HN21 URE sing 420 n n 
N2 HN22 URE sing 421 n n 
#
_atom_sites.entry_id                     1DDR 
_atom_sites.fract_transf_matrix[1][1]    0.010732 
_atom_sites.fract_transf_matrix[1][2]    0.006196 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012391 
_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]    0.013534 
_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 CL A 1 201 201 CL CL . 
D 3 MTX A 1 200 200 MTX MTX . 
E 4 URE A 1 211 211 URE URE . 
F 4 URE A 1 212 212 URE URE . 
G 4 URE A 1 213 213 URE URE . 
H 2 CL B 1 202 202 CL CL . 
I 5 CA B 1 203 203 CA CA . 
J 3 MTX B 1 200 200 MTX MTX . 
K 4 URE B 1 214 214 URE URE . 
L 4 URE B 1 215 215 URE URE . 
M 6 HOH A 1 701 701 HOH HOH . 
M 6 HOH A 2 702 702 HOH HOH . 
M 6 HOH A 3 703 703 HOH HOH . 
M 6 HOH A 4 704 704 HOH HOH . 
M 6 HOH A 5 705 705 HOH HOH . 
M 6 HOH A 6 706 706 HOH HOH . 
M 6 HOH A 7 707 707 HOH HOH . 
M 6 HOH A 8 708 708 HOH HOH . 
M 6 HOH A 9 709 709 HOH HOH . 
M 6 HOH A 10 710 710 HOH HOH . 
M 6 HOH A 11 711 711 HOH HOH . 
M 6 HOH A 12 712 712 HOH HOH . 
M 6 HOH A 13 713 713 HOH HOH . 
M 6 HOH A 14 714 714 HOH HOH . 
M 6 HOH A 15 715 715 HOH HOH . 
M 6 HOH A 16 716 716 HOH HOH . 
M 6 HOH A 17 717 717 HOH HOH . 
M 6 HOH A 18 718 718 HOH HOH . 
M 6 HOH A 19 719 719 HOH HOH . 
M 6 HOH A 20 720 720 HOH HOH . 
M 6 HOH A 21 721 721 HOH HOH . 
M 6 HOH A 22 722 722 HOH HOH . 
M 6 HOH A 23 723 723 HOH HOH . 
M 6 HOH A 24 724 724 HOH HOH . 
M 6 HOH A 25 725 725 HOH HOH . 
M 6 HOH A 26 727 727 HOH HOH . 
M 6 HOH A 27 728 728 HOH HOH . 
M 6 HOH A 28 729 729 HOH HOH . 
M 6 HOH A 29 730 730 HOH HOH . 
M 6 HOH A 30 731 731 HOH HOH . 
M 6 HOH A 31 732 732 HOH HOH . 
M 6 HOH A 32 734 734 HOH HOH . 
M 6 HOH A 33 735 735 HOH HOH . 
M 6 HOH A 34 736 736 HOH HOH . 
M 6 HOH A 35 737 737 HOH HOH . 
M 6 HOH A 36 738 738 HOH HOH . 
M 6 HOH A 37 739 739 HOH HOH . 
M 6 HOH A 38 740 740 HOH HOH . 
M 6 HOH A 39 741 741 HOH HOH . 
M 6 HOH A 40 742 742 HOH HOH . 
M 6 HOH A 41 753 753 HOH HOH . 
M 6 HOH A 42 780 780 HOH HOH . 
M 6 HOH A 43 781 781 HOH HOH . 
M 6 HOH A 44 782 782 HOH HOH . 
M 6 HOH A 45 783 783 HOH HOH . 
M 6 HOH A 46 788 788 HOH HOH . 
M 6 HOH A 47 794 794 HOH HOH . 
M 6 HOH A 48 795 795 HOH HOH . 
M 6 HOH A 49 796 796 HOH HOH . 
M 6 HOH A 50 797 797 HOH HOH . 
M 6 HOH A 51 798 798 HOH HOH . 
M 6 HOH A 52 799 799 HOH HOH . 
M 6 HOH A 53 800 800 HOH HOH . 
M 6 HOH A 54 801 801 HOH HOH . 
M 6 HOH A 55 802 802 HOH HOH . 
M 6 HOH A 56 804 804 HOH HOH . 
M 6 HOH A 57 805 805 HOH HOH . 
M 6 HOH A 58 806 806 HOH HOH . 
M 6 HOH A 59 807 807 HOH HOH . 
M 6 HOH A 60 809 809 HOH HOH . 
M 6 HOH A 61 810 810 HOH HOH . 
M 6 HOH A 62 811 811 HOH HOH . 
M 6 HOH A 63 812 812 HOH HOH . 
M 6 HOH A 64 814 814 HOH HOH . 
M 6 HOH A 65 815 815 HOH HOH . 
M 6 HOH A 66 816 816 HOH HOH . 
M 6 HOH A 67 817 817 HOH HOH . 
M 6 HOH A 68 818 818 HOH HOH . 
M 6 HOH A 69 819 819 HOH HOH . 
M 6 HOH A 70 820 820 HOH HOH . 
M 6 HOH A 71 821 821 HOH HOH . 
M 6 HOH A 72 822 822 HOH HOH . 
M 6 HOH A 73 823 823 HOH HOH . 
M 6 HOH A 74 824 824 HOH HOH . 
M 6 HOH A 75 825 825 HOH HOH . 
M 6 HOH A 76 826 826 HOH HOH . 
M 6 HOH A 77 827 827 HOH HOH . 
M 6 HOH A 78 828 828 HOH HOH . 
M 6 HOH A 79 829 829 HOH HOH . 
M 6 HOH A 80 830 830 HOH HOH . 
M 6 HOH A 81 833 833 HOH HOH . 
M 6 HOH A 82 834 834 HOH HOH . 
M 6 HOH A 83 835 835 HOH HOH . 
M 6 HOH A 84 836 836 HOH HOH . 
M 6 HOH A 85 837 837 HOH HOH . 
M 6 HOH A 86 838 838 HOH HOH . 
M 6 HOH A 87 839 839 HOH HOH . 
M 6 HOH A 88 840 840 HOH HOH . 
M 6 HOH A 89 860 860 HOH HOH . 
M 6 HOH A 90 861 861 HOH HOH . 
M 6 HOH A 91 862 862 HOH HOH . 
M 6 HOH A 92 863 863 HOH HOH . 
M 6 HOH A 93 864 864 HOH HOH . 
M 6 HOH A 94 868 868 HOH HOH . 
M 6 HOH A 95 875 875 HOH HOH . 
M 6 HOH A 96 876 876 HOH HOH . 
M 6 HOH A 97 877 877 HOH HOH . 
M 6 HOH A 98 878 878 HOH HOH . 
M 6 HOH A 99 879 879 HOH HOH . 
M 6 HOH A 100 880 880 HOH HOH . 
M 6 HOH A 101 881 881 HOH HOH . 
M 6 HOH A 102 882 882 HOH HOH . 
N 6 HOH B 1 733 733 HOH HOH . 
N 6 HOH B 2 743 743 HOH HOH . 
N 6 HOH B 3 744 744 HOH HOH . 
N 6 HOH B 4 745 745 HOH HOH . 
N 6 HOH B 5 746 746 HOH HOH . 
N 6 HOH B 6 747 747 HOH HOH . 
N 6 HOH B 7 748 748 HOH HOH . 
N 6 HOH B 8 749 749 HOH HOH . 
N 6 HOH B 9 750 750 HOH HOH . 
N 6 HOH B 10 751 751 HOH HOH . 
N 6 HOH B 11 752 752 HOH HOH . 
N 6 HOH B 12 754 754 HOH HOH . 
N 6 HOH B 13 756 756 HOH HOH . 
N 6 HOH B 14 757 757 HOH HOH . 
N 6 HOH B 15 758 758 HOH HOH . 
N 6 HOH B 16 759 759 HOH HOH . 
N 6 HOH B 17 760 760 HOH HOH . 
N 6 HOH B 18 761 761 HOH HOH . 
N 6 HOH B 19 762 762 HOH HOH . 
N 6 HOH B 20 763 763 HOH HOH . 
N 6 HOH B 21 764 764 HOH HOH . 
N 6 HOH B 22 765 765 HOH HOH . 
N 6 HOH B 23 766 766 HOH HOH . 
N 6 HOH B 24 767 767 HOH HOH . 
N 6 HOH B 25 768 768 HOH HOH . 
N 6 HOH B 26 769 769 HOH HOH . 
N 6 HOH B 27 770 770 HOH HOH . 
N 6 HOH B 28 771 771 HOH HOH . 
N 6 HOH B 29 772 772 HOH HOH . 
N 6 HOH B 30 773 773 HOH HOH . 
N 6 HOH B 31 774 774 HOH HOH . 
N 6 HOH B 32 775 775 HOH HOH . 
N 6 HOH B 33 776 776 HOH HOH . 
N 6 HOH B 34 777 777 HOH HOH . 
N 6 HOH B 35 778 778 HOH HOH . 
N 6 HOH B 36 779 779 HOH HOH . 
N 6 HOH B 37 784 784 HOH HOH . 
N 6 HOH B 38 785 785 HOH HOH . 
N 6 HOH B 39 786 786 HOH HOH . 
N 6 HOH B 40 787 787 HOH HOH . 
N 6 HOH B 41 789 789 HOH HOH . 
N 6 HOH B 42 790 790 HOH HOH . 
N 6 HOH B 43 791 791 HOH HOH . 
N 6 HOH B 44 792 792 HOH HOH . 
N 6 HOH B 45 793 793 HOH HOH . 
N 6 HOH B 46 803 803 HOH HOH . 
N 6 HOH B 47 808 808 HOH HOH . 
N 6 HOH B 48 813 813 HOH HOH . 
N 6 HOH B 49 831 831 HOH HOH . 
N 6 HOH B 50 832 832 HOH HOH . 
N 6 HOH B 51 841 841 HOH HOH . 
N 6 HOH B 52 842 842 HOH HOH . 
N 6 HOH B 53 843 843 HOH HOH . 
N 6 HOH B 54 844 844 HOH HOH . 
N 6 HOH B 55 845 845 HOH HOH . 
N 6 HOH B 56 846 846 HOH HOH . 
N 6 HOH B 57 847 847 HOH HOH . 
N 6 HOH B 58 848 848 HOH HOH . 
N 6 HOH B 59 849 849 HOH HOH . 
N 6 HOH B 60 850 850 HOH HOH . 
N 6 HOH B 61 851 851 HOH HOH . 
N 6 HOH B 62 852 852 HOH HOH . 
N 6 HOH B 63 854 854 HOH HOH . 
N 6 HOH B 64 855 855 HOH HOH . 
N 6 HOH B 65 856 856 HOH HOH . 
N 6 HOH B 66 857 857 HOH HOH . 
N 6 HOH B 67 858 858 HOH HOH . 
N 6 HOH B 68 859 859 HOH HOH . 
N 6 HOH B 69 865 865 HOH HOH . 
N 6 HOH B 70 866 866 HOH HOH . 
N 6 HOH B 71 867 867 HOH HOH . 
N 6 HOH B 72 869 869 HOH HOH . 
N 6 HOH B 73 870 870 HOH HOH . 
N 6 HOH B 74 871 871 HOH HOH . 
N 6 HOH B 75 872 872 HOH HOH . 
N 6 HOH B 76 873 873 HOH HOH . 
N 6 HOH B 77 874 874 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 C C URE . . . E 4 3.825 52.15 19.323 1 50 ? C URE 211 A 1 
HETATM 2 O O URE . . . E 4 4.328 51.767 20.371 1 50.4 ? O URE 211 A 1 
HETATM 3 N N1 URE . . . E 4 2.54 52.022 19.083 1 49.72 ? N1 URE 211 A 1 
HETATM 4 N N2 URE . . . E 4 4.553 52.675 18.345 1 48.54 ? N2 URE 211 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           268 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           4 
#