data_1AF2
#
_model_server_result.job_id            j9IPxC7FozQ_Bvq43xOamA 
_model_server_result.datetime_utc      '2025-04-11 14:42:34' 
_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          1af2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":295}' 
#
_entry.id    1AF2 
#
_exptl.entry_id    1AF2 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              324.181 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-MONOPHOSPHATE" 
_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            1AF2 
_cell.length_a            120.3 
_cell.length_b            120.3 
_cell.length_c            78.4 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1AF2 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31 2 1' 
#
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_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 A ND1 HIS 102 A HIS 102 1_555 B ZN ZN . A ZN 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? 
metalc ? metalc2 A SG CYS 129 A CYS 129 1_555 B ZN ZN . A ZN 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? 
metalc ? metalc3 A SG CYS 132 A CYS 132 1_555 B ZN ZN . A ZN 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? 
metalc ? metalc4 C O4 U5P . A U5P 295 1_555 B ZN ZN . A ZN 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
#
_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 358 n n 
N1 C6 U5P sing 359 n n 
N1 C1' U5P sing 360 n n 
C2 N3 U5P sing 361 n n 
C2 O2 U5P doub 362 n n 
N3 C4 U5P sing 363 n n 
N3 HN3 U5P sing 364 n n 
C4 C5 U5P sing 365 n n 
C4 O4 U5P doub 366 n n 
C5 C6 U5P doub 367 n n 
C5 H5 U5P sing 368 n n 
C6 H6 U5P sing 369 n n 
C1' C2' U5P sing 370 n n 
C1' O4' U5P sing 371 n n 
C1' H1' U5P sing 372 n n 
C2' O2' U5P sing 373 n n 
C2' C3' U5P sing 374 n n 
C2' H2' U5P sing 375 n n 
O2' HO2' U5P sing 376 n n 
C3' C4' U5P sing 377 n n 
C3' O3' U5P sing 378 n n 
C3' H3' U5P sing 379 n n 
C4' O4' U5P sing 380 n n 
C4' C5' U5P sing 381 n n 
C4' H4' U5P sing 382 n n 
O3' HO3' U5P sing 383 n n 
C5' O5' U5P sing 384 n n 
C5' "H5'1" U5P sing 385 n n 
C5' "H5'2" U5P sing 386 n n 
O5' P U5P sing 387 n n 
P O1P U5P doub 388 n n 
P O2P U5P sing 389 n n 
P O3P U5P sing 390 n n 
O2P HOP2 U5P sing 391 n n 
O3P HOP3 U5P sing 392 n n 
#
_atom_sites.entry_id                     1AF2 
_atom_sites.fract_transf_matrix[1][1]    0.008313 
_atom_sites.fract_transf_matrix[1][2]    0.004799 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009599 
_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]    0.012755 
_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
B 2 ZN A 1 296 296 ZN ZN . 
C 3 U5P A 1 295 295 U5P U . 
D 4 HOH A 1 503 503 HOH HOH . 
D 4 HOH A 2 505 505 HOH HOH . 
D 4 HOH A 3 506 506 HOH HOH . 
D 4 HOH A 4 509 509 HOH HOH . 
D 4 HOH A 5 511 511 HOH HOH . 
D 4 HOH A 6 515 515 HOH HOH . 
D 4 HOH A 7 516 516 HOH HOH . 
D 4 HOH A 8 517 517 HOH HOH . 
D 4 HOH A 9 518 518 HOH HOH . 
D 4 HOH A 10 522 522 HOH HOH . 
D 4 HOH A 11 525 525 HOH HOH . 
D 4 HOH A 12 526 526 HOH HOH . 
D 4 HOH A 13 527 527 HOH HOH . 
D 4 HOH A 14 528 528 HOH HOH . 
D 4 HOH A 15 531 531 HOH HOH . 
D 4 HOH A 16 533 533 HOH HOH . 
D 4 HOH A 17 536 536 HOH HOH . 
D 4 HOH A 18 538 538 HOH HOH . 
D 4 HOH A 19 539 539 HOH HOH . 
D 4 HOH A 20 540 540 HOH HOH . 
D 4 HOH A 21 541 541 HOH HOH . 
D 4 HOH A 22 542 542 HOH HOH . 
D 4 HOH A 23 550 550 HOH HOH . 
D 4 HOH A 24 555 555 HOH HOH . 
D 4 HOH A 25 557 557 HOH HOH . 
D 4 HOH A 26 558 558 HOH HOH . 
D 4 HOH A 27 560 560 HOH HOH . 
D 4 HOH A 28 561 561 HOH HOH . 
D 4 HOH A 29 562 562 HOH HOH . 
D 4 HOH A 30 563 563 HOH HOH . 
D 4 HOH A 31 564 564 HOH HOH . 
D 4 HOH A 32 565 565 HOH HOH . 
D 4 HOH A 33 566 566 HOH HOH . 
D 4 HOH A 34 568 568 HOH HOH . 
D 4 HOH A 35 569 569 HOH HOH . 
D 4 HOH A 36 573 573 HOH HOH . 
D 4 HOH A 37 575 575 HOH HOH . 
D 4 HOH A 38 601 601 HOH HOH . 
D 4 HOH A 39 602 602 HOH HOH . 
D 4 HOH A 40 603 603 HOH HOH . 
D 4 HOH A 41 604 604 HOH HOH . 
D 4 HOH A 42 605 605 HOH HOH . 
D 4 HOH A 43 607 607 HOH HOH . 
D 4 HOH A 44 610 610 HOH HOH . 
D 4 HOH A 45 611 611 HOH HOH . 
D 4 HOH A 46 613 613 HOH HOH . 
D 4 HOH A 47 615 615 HOH HOH . 
D 4 HOH A 48 616 616 HOH HOH . 
D 4 HOH A 49 617 617 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 . . . C 3 35.297 49.022 9.45 1.06 30.09 ? N1 U5P 295 A 1 
HETATM 2 C C2 U5P . . . C 3 36.066 48.356 8.522 1.06 31.38 ? C2 U5P 295 A 1 
HETATM 3 N N3 U5P . . . C 3 35.375 47.566 7.641 1.06 31.08 ? N3 U5P 295 A 1 
HETATM 4 C C4 U5P . . . C 3 34.015 47.499 7.496 1.06 26.09 ? C4 U5P 295 A 1 
HETATM 5 C C5 U5P . . . C 3 33.254 48.11 8.55 1.06 29.04 ? C5 U5P 295 A 1 
HETATM 6 C C6 U5P . . . C 3 33.869 48.852 9.484 1.06 25.42 ? C6 U5P 295 A 1 
HETATM 7 O O2 U5P . . . C 3 37.283 48.475 8.392 1.06 33.05 ? O2 U5P 295 A 1 
HETATM 8 O O4 U5P . . . C 3 33.586 46.981 6.505 1.06 22.89 ? O4 U5P 295 A 1 
HETATM 9 C C1' U5P . . . C 3 35.843 50.471 9.926 1.06 25.95 ? C1' U5P 295 A 1 
HETATM 10 C C2' U5P . . . C 3 35.865 51.864 9.382 1.06 25.64 ? C2' U5P 295 A 1 
HETATM 11 O O2' U5P . . . C 3 36.96 52.021 8.442 1.06 30.88 ? O2' U5P 295 A 1 
HETATM 12 C C3' U5P . . . C 3 36.078 52.588 10.632 1.06 27.15 ? C3' U5P 295 A 1 
HETATM 13 C C4' U5P . . . C 3 35.468 51.692 11.719 1.06 25.84 ? C4' U5P 295 A 1 
HETATM 14 O O3' U5P . . . C 3 37.463 52.729 10.819 1.06 24.67 ? O3' U5P 295 A 1 
HETATM 15 O O4' U5P . . . C 3 35.623 50.337 11.345 1.06 27.88 ? O4' U5P 295 A 1 
HETATM 16 C C5' U5P . . . C 3 34.09 52.06 12.104 1.06 27.67 ? C5' U5P 295 A 1 
HETATM 17 O O5' U5P . . . C 3 33.244 51.815 10.965 1.06 23.9 ? O5' U5P 295 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           334 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           17 
#