data_5MQL
#
_model_server_result.job_id            EUvNcXzeHScmYz90jlMyog 
_model_server_result.datetime_utc      '2024-11-22 08:26:07' 
_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          5mql 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":500}' 
#
_entry.id    5MQL 
#
_exptl.entry_id    5MQL 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    4 
_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            5MQL 
_cell.length_a            88.33 
_cell.length_b            88.33 
_cell.length_c            342.53 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5MQL 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 43 21 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 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F,G,H,M,N 1 1 
C,D,I,J,K,L,O,P 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
? 2 E N N 
? 2 G N N 
? 2 J N N 
? 2 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 C OG SER 64 C SER 35 1_555 I MG MG . C MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.964 ? 
metalc ? metalc2 C OE2 GLU 156 C GLU 127 1_555 I MG MG . C MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.982 ? 
metalc ? metalc3 I MG MG . C MG 301 1_555 K O1P DCM . C DCM 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? 
#
_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 463 n n 
N1 C6 UDP sing 464 n n 
N1 C1' UDP sing 465 n n 
C2 N3 UDP sing 466 n n 
C2 O2 UDP doub 467 n n 
N3 C4 UDP sing 468 n n 
N3 HN3 UDP sing 469 n n 
C4 C5 UDP sing 470 n n 
C4 O4 UDP doub 471 n n 
C5 C6 UDP doub 472 n n 
C5 H5 UDP sing 473 n n 
C6 H6 UDP sing 474 n n 
C1' C2' UDP sing 475 n n 
C1' O4' UDP sing 476 n n 
C1' H1' UDP sing 477 n n 
C2' O2' UDP sing 478 n n 
C2' C3' UDP sing 479 n n 
C2' H2' UDP sing 480 n n 
O2' HO2' UDP sing 481 n n 
C3' C4' UDP sing 482 n n 
C3' O3' UDP sing 483 n n 
C3' H3' UDP sing 484 n n 
C4' O4' UDP sing 485 n n 
C4' C5' UDP sing 486 n n 
C4' H4' UDP sing 487 n n 
O3' HO3' UDP sing 488 n n 
C5' O5' UDP sing 489 n n 
C5' "H5'1" UDP sing 490 n n 
C5' "H5'2" UDP sing 491 n n 
O5' PA UDP sing 492 n n 
PA O1A UDP doub 493 n n 
PA O2A UDP sing 494 n n 
PA O3A UDP sing 495 n n 
O2A HOA2 UDP sing 496 n n 
O3A PB UDP sing 497 n n 
PB O1B UDP doub 498 n n 
PB O2B UDP sing 499 n n 
PB O3B UDP sing 500 n n 
O2B HOB2 UDP sing 501 n n 
O3B HOB3 UDP sing 502 n n 
#
_atom_sites.entry_id                     5MQL 
_atom_sites.fract_transf_matrix[1][1]    0.011321 
_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]    0.011321 
_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]    0.002919 
_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
E 2 UDP A 1 301 500 UDP UDP . 
F 3 G65 A 1 302 600 G65 DRG . 
G 2 UDP B 1 301 500 UDP UDP . 
H 4 DCM B 1 302 550 DCM DCM . 
I 5 MG C 1 301 450 MG MG . 
J 2 UDP C 1 302 500 UDP UDP . 
K 4 DCM C 1 303 550 DCM DCM . 
L 2 UDP D 1 500 500 UDP UDP . 
M 6 HOH A 1 401 8 HOH HOH . 
M 6 HOH A 2 402 5 HOH HOH . 
M 6 HOH A 3 403 14 HOH HOH . 
M 6 HOH A 4 404 6 HOH HOH . 
M 6 HOH A 5 405 9 HOH HOH . 
N 6 HOH B 1 401 13 HOH HOH . 
N 6 HOH B 2 402 3 HOH HOH . 
N 6 HOH B 3 403 11 HOH HOH . 
O 6 HOH C 1 401 10 HOH HOH . 
O 6 HOH C 2 402 4 HOH HOH . 
O 6 HOH C 3 403 1 HOH HOH . 
O 6 HOH C 4 404 15 HOH HOH . 
O 6 HOH C 5 405 7 HOH HOH . 
P 6 HOH D 1 601 2 HOH HOH . 
P 6 HOH D 2 602 12 HOH HOH . 
P 6 HOH D 3 603 17 HOH HOH . 
P 6 HOH D 4 604 16 HOH HOH . 
P 6 HOH D 5 605 18 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 . . . L 2 -16.938 16.255 27.602 1 102.2 ? N1 UDP 500 D 1 
HETATM 2 C C2 UDP . . . L 2 -17.998 15.373 27.56 1 104.43 ? C2 UDP 500 D 1 
HETATM 3 N N3 UDP . . . L 2 -17.819 14.292 26.728 1 104.47 ? N3 UDP 500 D 1 
HETATM 4 C C4 UDP . . . L 2 -16.716 14.024 25.94 1 102.55 ? C4 UDP 500 D 1 
HETATM 5 C C5 UDP . . . L 2 -15.655 14.975 26.05 1 99.99 ? C5 UDP 500 D 1 
HETATM 6 C C6 UDP . . . L 2 -15.791 16.034 26.863 1 100.08 ? C6 UDP 500 D 1 
HETATM 7 O O2 UDP . . . L 2 -19.038 15.547 28.18 1 106.71 ? O2 UDP 500 D 1 
HETATM 8 O O4 UDP . . . L 2 -16.725 13.046 25.188 1 103.72 ? O4 UDP 500 D 1 
HETATM 9 C C1' UDP . . . L 2 -17.083 17.468 28.416 1 102.65 ? C1' UDP 500 D 1 
HETATM 10 C C2' UDP . . . L 2 -16.231 17.449 29.681 1 103.03 ? C2' UDP 500 D 1 
HETATM 11 O O2' UDP . . . L 2 -16.935 16.819 30.749 1 106.22 ? O2' UDP 500 D 1 
HETATM 12 C C3' UDP . . . L 2 -15.929 18.941 29.894 1 101.84 ? C3' UDP 500 D 1 
HETATM 13 C C4' UDP . . . L 2 -15.964 19.524 28.482 1 100.13 ? C4' UDP 500 D 1 
HETATM 14 O O4' UDP . . . L 2 -16.644 18.568 27.647 1 100.39 ? O4' UDP 500 D 1 
HETATM 15 O O3' UDP . . . L 2 -16.844 19.611 30.752 1 104.23 ? O3' UDP 500 D 1 
HETATM 16 C C5' UDP . . . L 2 -14.632 19.866 27.868 1 98.92 ? C5' UDP 500 D 1 
HETATM 17 O O5' UDP . . . L 2 -13.709 18.764 27.972 1 99.74 ? O5' UDP 500 D 1 
HETATM 18 P PA UDP . . . L 2 -12.229 18.946 28.531 1 100.07 ? PA UDP 500 D 1 
HETATM 19 O O1A UDP . . . L 2 -11.46 17.642 28.271 1 99.07 ? O1A UDP 500 D 1 
HETATM 20 O O2A UDP . . . L 2 -12.261 19.268 29.978 1 100.51 ? O2A UDP 500 D 1 
HETATM 21 O O3A UDP . . . L 2 -11.546 20.145 27.722 1 100.99 ? O3A UDP 500 D 1 
HETATM 22 P PB UDP . . . L 2 -10.13 20.42 27.033 1 101.24 ? PB UDP 500 D 1 
HETATM 23 O O1B UDP . . . L 2 -10.099 19.571 25.775 1 100.72 ? O1B UDP 500 D 1 
HETATM 24 O O2B UDP . . . L 2 -8.923 20.213 27.961 1 100.8 ? O2B UDP 500 D 1 
HETATM 25 O O3B UDP . . . L 2 -10.134 21.853 26.508 1 101.54 ? O3B UDP 500 D 1 
#
_model_server_stats.io_time_ms              61 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           634 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           25 
#