data_3ERC
#
_model_server_result.job_id            -gCmJfLzXO3ge17oVencSw 
_model_server_result.datetime_utc      '2024-11-13 17:31:25' 
_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          3erc 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":602}' 
#
_entry.id    3ERC 
#
_exptl.entry_id    3ERC 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              324.181 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-MONOPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         89.52 
_cell.angle_beta          73.45 
_cell.angle_gamma         63.76 
_cell.entry_id            3ERC 
_cell.length_a            69.925 
_cell.length_b            77.153 
_cell.length_c            108.03 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3ERC 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
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 tetrameric 4 author_and_software_defined_assembly 1 
PISA tetrameric 4 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,H,M,N,O,P 1 1 
B,C,F,G,I,J,K,L,Q 2 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
? 6 I N N 
? 6 M 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 C OD1 ASP 202 C ASP 202 1_555 K CA CA . C CA 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.709 ? 
metalc ? metalc2 C OD1 ASP 202 C ASP 202 1_555 L CA CA . C CA 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.815 ? 
metalc ? metalc3 C OD2 ASP 202 C ASP 202 1_555 L CA CA . C CA 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.614 ? 
metalc ? metalc4 C OD1 ASP 204 C ASP 204 1_555 K CA CA . C CA 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.706 ? 
metalc ? metalc5 C OD1 ASP 204 C ASP 204 1_555 L CA CA . C CA 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? 
metalc ? metalc6 C OD2 ASP 204 C ASP 204 1_555 L CA CA . C CA 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? 
metalc ? metalc7 C OD1 ASP 253 C ASP 253 1_555 K CA CA . C CA 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.911 ? 
metalc ? metalc8 C OD2 ASP 253 C ASP 253 1_555 K CA CA . C CA 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? 
metalc ? metalc9 J O1G 3AT . C 3AT 801 1_555 L CA CA . C CA 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.61 ? 
metalc ? metalc10 J O1B 3AT . C 3AT 801 1_555 L CA CA . C CA 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? 
metalc ? metalc11 J O1A 3AT . C 3AT 801 1_555 L CA CA . C CA 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? 
metalc ? metalc12 K CA CA . C CA 901 1_555 F O3' DC 5 F DC 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.822 ? 
metalc ? metalc13 D OD1 ASP 202 D ASP 202 1_555 O CA CA . D CA 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? 
metalc ? metalc14 D OD1 ASP 202 D ASP 202 1_555 P CA CA . D CA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.961 ? 
metalc ? metalc15 D OD2 ASP 202 D ASP 202 1_555 P CA CA . D CA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? 
metalc ? metalc16 D OD1 ASP 204 D ASP 204 1_555 O CA CA . D CA 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.533 ? 
metalc ? metalc17 D OD1 ASP 204 D ASP 204 1_555 P CA CA . D CA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.706 ? 
metalc ? metalc18 D OD2 ASP 204 D ASP 204 1_555 P CA CA . D CA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
metalc ? metalc19 D OD1 ASP 253 D ASP 253 1_555 O CA CA . D CA 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? 
metalc ? metalc20 D OD2 ASP 253 D ASP 253 1_555 O CA CA . D CA 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? 
metalc ? metalc21 N O1G 3AT . D 3AT 800 1_555 P CA CA . D CA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? 
metalc ? metalc22 N O1B 3AT . D 3AT 800 1_555 P CA CA . D CA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? 
metalc ? metalc23 N O1A 3AT . D 3AT 800 1_555 P CA CA . D CA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.614 ? 
metalc ? metalc24 O CA CA . D CA 903 1_555 E O3' DC 5 E DC 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? 
#
_chem_comp.formula           'C9 H13 N2 O9 P' 
_chem_comp.formula_weight    324.181 
_chem_comp.id                U5P 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-MONOPHOSPHATE" 
_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
N1 C2 U5P sing 476 n n 
N1 C6 U5P sing 477 n n 
N1 C1' U5P sing 478 n n 
C2 N3 U5P sing 479 n n 
C2 O2 U5P doub 480 n n 
N3 C4 U5P sing 481 n n 
N3 HN3 U5P sing 482 n n 
C4 C5 U5P sing 483 n n 
C4 O4 U5P doub 484 n n 
C5 C6 U5P doub 485 n n 
C5 H5 U5P sing 486 n n 
C6 H6 U5P sing 487 n n 
C1' C2' U5P sing 488 n n 
C1' O4' U5P sing 489 n n 
C1' H1' U5P sing 490 n n 
C2' O2' U5P sing 491 n n 
C2' C3' U5P sing 492 n n 
C2' H2' U5P sing 493 n n 
O2' HO2' U5P sing 494 n n 
C3' C4' U5P sing 495 n n 
C3' O3' U5P sing 496 n n 
C3' H3' U5P sing 497 n n 
C4' O4' U5P sing 498 n n 
C4' C5' U5P sing 499 n n 
C4' H4' U5P sing 500 n n 
O3' HO3' U5P sing 501 n n 
C5' O5' U5P sing 502 n n 
C5' "H5'1" U5P sing 503 n n 
C5' "H5'2" U5P sing 504 n n 
O5' P U5P sing 505 n n 
P O1P U5P doub 506 n n 
P O2P U5P sing 507 n n 
P O3P U5P sing 508 n n 
O2P HOP2 U5P sing 509 n n 
O3P HOP3 U5P sing 510 n n 
#
_atom_sites.entry_id                     3ERC 
_atom_sites.fract_transf_matrix[1][1]    0.014301 
_atom_sites.fract_transf_matrix[1][2]    -0.007049 
_atom_sites.fract_transf_matrix[1][3]    -0.005263 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01445 
_atom_sites.fract_transf_matrix[2][3]    0.001995 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.009748 
_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
I 6 U5P C 1 600 600 U5P U . 
J 7 3AT C 1 801 801 3AT 3AT . 
K 8 CA C 1 901 901 CA CA . 
L 8 CA C 1 902 902 CA CA . 
M 6 U5P D 1 602 602 U5P U . 
N 7 3AT D 1 800 800 3AT 3AT . 
O 8 CA D 1 903 903 CA CA . 
P 8 CA D 1 904 904 CA CA . 
Q 9 HOH C 1 1001 1001 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 U5P . . . M 6 -14.473 -2.631 22.431 1 79.76 ? N1 U5P 602 D 1 
HETATM 2 C C2 U5P . . . M 6 -14.148 -3.921 22.855 1 79.76 ? C2 U5P 602 D 1 
HETATM 3 N N3 U5P . . . M 6 -13.441 -4.668 21.938 1 79.76 ? N3 U5P 602 D 1 
HETATM 4 C C4 U5P . . . M 6 -13.049 -4.285 20.66 1 79.76 ? C4 U5P 602 D 1 
HETATM 5 C C5 U5P . . . M 6 -13.457 -2.965 20.277 1 79.76 ? C5 U5P 602 D 1 
HETATM 6 C C6 U5P . . . M 6 -14.137 -2.201 21.149 1 79.76 ? C6 U5P 602 D 1 
HETATM 7 O O2 U5P . . . M 6 -14.468 -4.371 23.948 1 79.76 ? O2 U5P 602 D 1 
HETATM 8 O O4 U5P . . . M 6 -12.364 -5.057 19.978 1 79.76 ? O4 U5P 602 D 1 
HETATM 9 C C1' U5P . . . M 6 -15.155 -1.733 23.386 1 79.76 ? C1' U5P 602 D 1 
HETATM 10 C C2' U5P . . . M 6 -15.203 -0.26 22.956 1 79.76 ? C2' U5P 602 D 1 
HETATM 11 O O2' U5P . . . M 6 -14.025 0.45 23.307 1 79.76 ? O2' U5P 602 D 1 
HETATM 12 C C3' U5P . . . M 6 -16.448 0.226 23.692 1 79.76 ? C3' U5P 602 D 1 
HETATM 13 C C4' U5P . . . M 6 -17.381 -0.985 23.582 1 79.76 ? C4' U5P 602 D 1 
HETATM 14 O O3' U5P . . . M 6 -16.026 0.409 25.05 1 79.76 ? O3' U5P 602 D 1 
HETATM 15 O O4' U5P . . . M 6 -16.505 -2.152 23.512 1 79.76 ? O4' U5P 602 D 1 
HETATM 16 C C5' U5P . . . M 6 -18.347 -1.02 22.401 1 79.76 ? C5' U5P 602 D 1 
HETATM 17 O O5' U5P . . . M 6 -17.642 -1.338 21.168 1 79.76 ? O5' U5P 602 D 1 
HETATM 18 P P U5P . . . M 6 -18.314 -2.301 20.027 1 79.76 ? P U5P 602 D 1 
HETATM 19 O O1P U5P . . . M 6 -18.049 -3.749 20.462 1 79.76 ? O1P U5P 602 D 1 
HETATM 20 O O2P U5P . . . M 6 -17.582 -1.97 18.724 1 79.76 ? O2P U5P 602 D 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           315 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           20 
#