data_2IER
#
_model_server_result.job_id            1pJEynCpf7eww1j7yO41Jg 
_model_server_result.datetime_utc      '2024-12-01 03:39:38' 
_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          2ier 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":802}' 
#
_entry.id    2IER 
#
_exptl.entry_id    2IER 
_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         120 
_cell.entry_id            2IER 
_cell.length_a            101.206 
_cell.length_b            101.206 
_cell.length_c            122.24 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2IER 
_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,O,P,Q,R 
_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
? 3 H N N 
? 3 O 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 N GLY 2 A GLY 2 1_555 E ZN ZN . A ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? 
metalc ? metalc2 A NE2 HIS 58 A HIS 58 1_555 D ZN ZN . A ZN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? 
metalc ? metalc3 A ND1 HIS 58 A HIS 58 1_555 G ZN ZN . A ZN 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? 
metalc ? metalc4 A OE2 GLU 73 A GLU 78 1_555 F ZN ZN . A ZN 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? 
metalc ? metalc5 A NE2 HIS 74 A HIS 79 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? 
metalc ? metalc6 A OE1 GLU 120 A GLU 126 1_555 E ZN ZN . A ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? 
metalc ? metalc7 A OE2 GLU 120 A GLU 126 1_555 E ZN ZN . A ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? 
metalc ? metalc8 A NE2 HIS 188 A HIS 200 1_555 D ZN ZN . A ZN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? 
metalc ? metalc9 A NE2 HIS 226 A HIS 238 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? 
metalc ? metalc10 A OD1 ASP 230 A ASP 242 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc11 A NE2 HIS 253 A HIS 265 1_555 F ZN ZN . A ZN 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? 
metalc ? metalc12 C ZN ZN . A ZN 601 1_555 Q O HOH . A HOH 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? 
metalc ? metalc13 E ZN ZN . A ZN 605 1_555 B NE2 HIS 29 B HIS 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
metalc ? metalc14 E ZN ZN . A ZN 605 1_555 B OE1 GLU 90 B GLU 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? 
metalc ? metalc15 E ZN ZN . A ZN 605 1_555 B OE2 GLU 90 B GLU 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.687 ? 
metalc ? metalc16 F ZN ZN . A ZN 606 1_555 Q O HOH . A HOH 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? 
metalc ? metalc17 F ZN ZN . A ZN 606 1_555 Q O HOH . A HOH 830 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
metalc ? metalc18 G ZN ZN . A ZN 608 1_555 H O2B UDP . A UDP 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? 
metalc ? metalc19 B NE2 HIS 58 B HIS 58 1_555 L ZN ZN . B ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? 
metalc ? metalc20 B ND1 HIS 58 B HIS 58 1_555 N ZN ZN . B ZN 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? 
metalc ? metalc21 B OE2 GLU 73 B GLU 78 1_555 M ZN ZN . B ZN 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
metalc ? metalc22 B NE2 HIS 74 B HIS 79 1_555 K ZN ZN . B ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? 
metalc ? metalc23 B NE2 HIS 188 B HIS 200 1_555 L ZN ZN . B ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? 
metalc ? metalc24 B NE2 HIS 226 B HIS 238 1_555 K ZN ZN . B ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? 
metalc ? metalc25 B OD1 ASP 230 B ASP 242 1_555 K ZN ZN . B ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
metalc ? metalc26 B NE2 HIS 253 B HIS 265 1_555 M ZN ZN . B ZN 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? 
metalc ? metalc27 K ZN ZN . B ZN 602 1_555 R O HOH . B HOH 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.885 ? 
metalc ? metalc28 M ZN ZN . B ZN 607 1_555 R O HOH . B HOH 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.787 ? 
metalc ? metalc29 N ZN ZN . B ZN 609 1_555 O O3A UDP . B UDP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.711 ? 
metalc ? metalc30 N ZN ZN . B ZN 609 1_555 O O2B UDP . B UDP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? 
#
_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 420 n n 
N1 C6 UDP sing 421 n n 
N1 C1' UDP sing 422 n n 
C2 N3 UDP sing 423 n n 
C2 O2 UDP doub 424 n n 
N3 C4 UDP sing 425 n n 
N3 HN3 UDP sing 426 n n 
C4 C5 UDP sing 427 n n 
C4 O4 UDP doub 428 n n 
C5 C6 UDP doub 429 n n 
C5 H5 UDP sing 430 n n 
C6 H6 UDP sing 431 n n 
C1' C2' UDP sing 432 n n 
C1' O4' UDP sing 433 n n 
C1' H1' UDP sing 434 n n 
C2' O2' UDP sing 435 n n 
C2' C3' UDP sing 436 n n 
C2' H2' UDP sing 437 n n 
O2' HO2' UDP sing 438 n n 
C3' C4' UDP sing 439 n n 
C3' O3' UDP sing 440 n n 
C3' H3' UDP sing 441 n n 
C4' O4' UDP sing 442 n n 
C4' C5' UDP sing 443 n n 
C4' H4' UDP sing 444 n n 
O3' HO3' UDP sing 445 n n 
C5' O5' UDP sing 446 n n 
C5' "H5'1" UDP sing 447 n n 
C5' "H5'2" UDP sing 448 n n 
O5' PA UDP sing 449 n n 
PA O1A UDP doub 450 n n 
PA O2A UDP sing 451 n n 
PA O3A UDP sing 452 n n 
O2A HOA2 UDP sing 453 n n 
O3A PB UDP sing 454 n n 
PB O1B UDP doub 455 n n 
PB O2B UDP sing 456 n n 
PB O3B UDP sing 457 n n 
O2B HOB2 UDP sing 458 n n 
O3B HOB3 UDP sing 459 n n 
#
_atom_sites.entry_id                     2IER 
_atom_sites.fract_transf_matrix[1][1]    0.009881 
_atom_sites.fract_transf_matrix[1][2]    0.005705 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011409 
_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]    0.008181 
_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 ZN A 1 601 601 ZN ZN . 
D 2 ZN A 1 603 603 ZN ZN . 
E 2 ZN A 1 605 605 ZN ZN . 
F 2 ZN A 1 606 606 ZN ZN . 
G 2 ZN A 1 608 608 ZN ZN . 
H 3 UDP A 1 801 801 UDP UDP . 
I 4 PLM A 1 701 701 PLM PLM . 
J 5 GOL A 1 501 501 GOL GOL . 
K 2 ZN B 1 602 602 ZN ZN . 
L 2 ZN B 1 604 604 ZN ZN . 
M 2 ZN B 1 607 607 ZN ZN . 
N 2 ZN B 1 609 609 ZN ZN . 
O 3 UDP B 1 802 802 UDP UDP . 
P 4 PLM B 1 702 702 PLM PLM . 
Q 6 HOH A 1 802 1 HOH HOH . 
Q 6 HOH A 2 803 3 HOH HOH . 
Q 6 HOH A 3 804 4 HOH HOH . 
Q 6 HOH A 4 805 5 HOH HOH . 
Q 6 HOH A 5 806 6 HOH HOH . 
Q 6 HOH A 6 807 9 HOH HOH . 
Q 6 HOH A 7 808 11 HOH HOH . 
Q 6 HOH A 8 809 16 HOH HOH . 
Q 6 HOH A 9 810 17 HOH HOH . 
Q 6 HOH A 10 811 20 HOH HOH . 
Q 6 HOH A 11 812 21 HOH HOH . 
Q 6 HOH A 12 813 23 HOH HOH . 
Q 6 HOH A 13 814 24 HOH HOH . 
Q 6 HOH A 14 815 25 HOH HOH . 
Q 6 HOH A 15 816 26 HOH HOH . 
Q 6 HOH A 16 817 27 HOH HOH . 
Q 6 HOH A 17 818 31 HOH HOH . 
Q 6 HOH A 18 819 34 HOH HOH . 
Q 6 HOH A 19 820 36 HOH HOH . 
Q 6 HOH A 20 821 37 HOH HOH . 
Q 6 HOH A 21 822 38 HOH HOH . 
Q 6 HOH A 22 823 40 HOH HOH . 
Q 6 HOH A 23 824 41 HOH HOH . 
Q 6 HOH A 24 825 42 HOH HOH . 
Q 6 HOH A 25 826 43 HOH HOH . 
Q 6 HOH A 26 827 47 HOH HOH . 
Q 6 HOH A 27 828 49 HOH HOH . 
Q 6 HOH A 28 829 50 HOH HOH . 
Q 6 HOH A 29 830 53 HOH HOH . 
Q 6 HOH A 30 831 55 HOH HOH . 
Q 6 HOH A 31 832 61 HOH HOH . 
Q 6 HOH A 32 833 64 HOH HOH . 
Q 6 HOH A 33 834 67 HOH HOH . 
Q 6 HOH A 34 835 68 HOH HOH . 
Q 6 HOH A 35 836 70 HOH HOH . 
Q 6 HOH A 36 837 71 HOH HOH . 
Q 6 HOH A 37 838 73 HOH HOH . 
Q 6 HOH A 38 839 74 HOH HOH . 
Q 6 HOH A 39 840 75 HOH HOH . 
Q 6 HOH A 40 841 76 HOH HOH . 
Q 6 HOH A 41 842 77 HOH HOH . 
Q 6 HOH A 42 843 86 HOH HOH . 
R 6 HOH B 1 803 2 HOH HOH . 
R 6 HOH B 2 804 7 HOH HOH . 
R 6 HOH B 3 805 8 HOH HOH . 
R 6 HOH B 4 806 10 HOH HOH . 
R 6 HOH B 5 807 12 HOH HOH . 
R 6 HOH B 6 808 13 HOH HOH . 
R 6 HOH B 7 809 14 HOH HOH . 
R 6 HOH B 8 810 15 HOH HOH . 
R 6 HOH B 9 811 18 HOH HOH . 
R 6 HOH B 10 812 19 HOH HOH . 
R 6 HOH B 11 813 28 HOH HOH . 
R 6 HOH B 12 814 29 HOH HOH . 
R 6 HOH B 13 815 30 HOH HOH . 
R 6 HOH B 14 816 32 HOH HOH . 
R 6 HOH B 15 817 35 HOH HOH . 
R 6 HOH B 16 818 39 HOH HOH . 
R 6 HOH B 17 819 44 HOH HOH . 
R 6 HOH B 18 820 45 HOH HOH . 
R 6 HOH B 19 821 46 HOH HOH . 
R 6 HOH B 20 822 48 HOH HOH . 
R 6 HOH B 21 823 51 HOH HOH . 
R 6 HOH B 22 824 52 HOH HOH . 
R 6 HOH B 23 825 54 HOH HOH . 
R 6 HOH B 24 826 56 HOH HOH . 
R 6 HOH B 25 827 57 HOH HOH . 
R 6 HOH B 26 828 58 HOH HOH . 
R 6 HOH B 27 829 59 HOH HOH . 
R 6 HOH B 28 830 60 HOH HOH . 
R 6 HOH B 29 831 62 HOH HOH . 
R 6 HOH B 30 832 63 HOH HOH . 
R 6 HOH B 31 833 65 HOH HOH . 
R 6 HOH B 32 834 69 HOH HOH . 
R 6 HOH B 33 835 72 HOH HOH . 
R 6 HOH B 34 836 79 HOH HOH . 
R 6 HOH B 35 837 85 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 . . . O 3 50.501 71.39 11.893 1 49.56 ? N1 UDP 802 B 1 
HETATM 2 C C2 UDP . . . O 3 51.562 72.185 12.361 1 50.07 ? C2 UDP 802 B 1 
HETATM 3 N N3 UDP . . . O 3 52.854 71.797 12.046 1 49.82 ? N3 UDP 802 B 1 
HETATM 4 C C4 UDP . . . O 3 53.148 70.665 11.294 1 49.2 ? C4 UDP 802 B 1 
HETATM 5 C C5 UDP . . . O 3 52.082 69.867 10.825 1 48.95 ? C5 UDP 802 B 1 
HETATM 6 C C6 UDP . . . O 3 50.758 70.238 11.13 1 48.53 ? C6 UDP 802 B 1 
HETATM 7 O O2 UDP . . . O 3 51.412 73.224 13.048 1 49.92 ? O2 UDP 802 B 1 
HETATM 8 O O4 UDP . . . O 3 54.348 70.42 11.075 1 50.62 ? O4 UDP 802 B 1 
HETATM 9 C C1' UDP . . . O 3 49.096 71.787 12.22 1 50.26 ? C1' UDP 802 B 1 
HETATM 10 C C2' UDP . . . O 3 48.324 72.527 11.116 1 49.93 ? C2' UDP 802 B 1 
HETATM 11 O O2' UDP . . . O 3 48.722 73.879 10.976 1 50.09 ? O2' UDP 802 B 1 
HETATM 12 C C3' UDP . . . O 3 46.888 72.277 11.551 1 50.29 ? C3' UDP 802 B 1 
HETATM 13 C C4' UDP . . . O 3 46.924 70.976 12.495 1 50.41 ? C4' UDP 802 B 1 
HETATM 14 O O4' UDP . . . O 3 48.309 70.636 12.547 1 50.66 ? O4' UDP 802 B 1 
HETATM 15 O O3' UDP . . . O 3 46.435 73.213 12.501 1 49.32 ? O3' UDP 802 B 1 
HETATM 16 C C5' UDP . . . O 3 46.147 69.909 11.684 1 51.59 ? C5' UDP 802 B 1 
HETATM 17 O O5' UDP . . . O 3 45.677 70.384 10.414 1 53.27 ? O5' UDP 802 B 1 
HETATM 18 P PA UDP . . . O 3 46.246 69.903 8.973 1 50.35 ? PA UDP 802 B 1 
HETATM 19 O O1A UDP . . . O 3 47.427 69.034 9.164 1 51.6 ? O1A UDP 802 B 1 
HETATM 20 O O2A UDP . . . O 3 46.539 71.118 8.171 1 52.77 ? O2A UDP 802 B 1 
HETATM 21 O O3A UDP . . . O 3 45.087 68.981 8.331 1 52.11 ? O3A UDP 802 B 1 
HETATM 22 P PB UDP . . . O 3 44.819 67.397 8.076 1 51.31 ? PB UDP 802 B 1 
HETATM 23 O O1B UDP . . . O 3 44.373 67.381 6.641 1 51.67 ? O1B UDP 802 B 1 
HETATM 24 O O2B UDP . . . O 3 43.72 67.055 9.016 1 50.85 ? O2B UDP 802 B 1 
HETATM 25 O O3B UDP . . . O 3 46.066 66.602 8.25 1 48.5 ? O3B UDP 802 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           293 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#