data_2RNF
#
_model_server_result.job_id            IVEZCbPO26ozBT8V83SWGA 
_model_server_result.datetime_utc      '2025-04-06 00:45:07' 
_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          2rnf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":302}' 
#
_entry.id    2RNF 
#
_exptl.entry_id    2RNF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              308.182 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXYURIDINE 3'-MONOPHOSPHATE" 
_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          107.2 
_cell.angle_gamma         90 
_cell.entry_id            2RNF 
_cell.length_a            32.83 
_cell.length_b            94.33 
_cell.length_c            40.66 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2RNF 
_symmetry.cell_setting             monoclinic 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E 1 1 
B,D,F 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 C N N 
? 2 D 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
disulf ? disulf1 A SG CYS 26 A CYS 25 1_555 A SG CYS 82 A CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
disulf ? disulf2 A SG CYS 40 A CYS 39 1_555 A SG CYS 93 A CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? 
disulf ? disulf3 A SG CYS 58 A CYS 57 1_555 A SG CYS 108 A CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? 
disulf ? disulf4 A SG CYS 65 A CYS 64 1_555 A SG CYS 72 A CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
disulf ? disulf5 B SG CYS 26 B CYS 25 1_555 B SG CYS 82 B CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? 
disulf ? disulf6 B SG CYS 40 B CYS 39 1_555 B SG CYS 93 B CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
disulf ? disulf7 B SG CYS 58 B CYS 57 1_555 B SG CYS 108 B CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf8 B SG CYS 65 B CYS 64 1_555 B SG CYS 72 B CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
#
_chem_comp.formula           'C9 H13 N2 O8 P' 
_chem_comp.formula_weight    308.182 
_chem_comp.id                UM3 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-DEOXYURIDINE 3'-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 UM3 sing 358 n y 
N1 C6 UM3 sing 359 n y 
N1 C1' UM3 sing 360 n n 
C2 N3 UM3 sing 361 n y 
C2 O2 UM3 doub 362 n n 
N3 C4 UM3 sing 363 n y 
N3 HN3 UM3 sing 364 n n 
C4 C5 UM3 sing 365 n y 
C4 O4 UM3 doub 366 n n 
C5 C6 UM3 doub 367 n y 
C5 H5 UM3 sing 368 n n 
C6 H6 UM3 sing 369 n n 
C1' C2' UM3 sing 370 n n 
C1' O4' UM3 sing 371 n n 
C1' H1' UM3 sing 372 n n 
C2' C3' UM3 sing 373 n n 
C2' "H2'1" UM3 sing 374 n n 
C2' "H2'2" UM3 sing 375 n n 
C3' C4' UM3 sing 376 n n 
C3' O3' UM3 sing 377 n n 
C3' H3' UM3 sing 378 n n 
C4' O4' UM3 sing 379 n n 
C4' C5' UM3 sing 380 n n 
C4' H4' UM3 sing 381 n n 
O3' P UM3 sing 382 n n 
C5' O5' UM3 sing 383 n n 
C5' "H5'1" UM3 sing 384 n n 
C5' "H5'2" UM3 sing 385 n n 
O5' HO5' UM3 sing 386 n n 
P O1P UM3 doub 387 n n 
P O2P UM3 sing 388 n n 
P O3P UM3 sing 389 n n 
O2P HOP2 UM3 sing 390 n n 
O3P HOP3 UM3 sing 391 n n 
#
_atom_sites.entry_id                     2RNF 
_atom_sites.fract_transf_matrix[1][1]    0.03046 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.009429 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010601 
_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]    0.025745 
_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 UM3 A 1 301 301 UM3 UM3 . 
D 2 UM3 B 1 302 302 UM3 UM3 . 
E 3 HOH A 1 302 1 HOH HOH . 
E 3 HOH A 2 303 4 HOH HOH . 
E 3 HOH A 3 304 5 HOH HOH . 
E 3 HOH A 4 305 6 HOH HOH . 
E 3 HOH A 5 306 7 HOH HOH . 
E 3 HOH A 6 307 8 HOH HOH . 
E 3 HOH A 7 308 9 HOH HOH . 
E 3 HOH A 8 309 10 HOH HOH . 
E 3 HOH A 9 310 13 HOH HOH . 
E 3 HOH A 10 311 14 HOH HOH . 
E 3 HOH A 11 312 15 HOH HOH . 
E 3 HOH A 12 313 16 HOH HOH . 
E 3 HOH A 13 314 17 HOH HOH . 
E 3 HOH A 14 315 18 HOH HOH . 
E 3 HOH A 15 316 19 HOH HOH . 
E 3 HOH A 16 317 20 HOH HOH . 
E 3 HOH A 17 318 21 HOH HOH . 
E 3 HOH A 18 319 22 HOH HOH . 
E 3 HOH A 19 320 23 HOH HOH . 
E 3 HOH A 20 321 28 HOH HOH . 
E 3 HOH A 21 322 29 HOH HOH . 
E 3 HOH A 22 323 30 HOH HOH . 
E 3 HOH A 23 324 31 HOH HOH . 
E 3 HOH A 24 325 32 HOH HOH . 
E 3 HOH A 25 326 36 HOH HOH . 
E 3 HOH A 26 327 37 HOH HOH . 
E 3 HOH A 27 328 38 HOH HOH . 
E 3 HOH A 28 329 39 HOH HOH . 
E 3 HOH A 29 330 41 HOH HOH . 
E 3 HOH A 30 331 42 HOH HOH . 
E 3 HOH A 31 332 43 HOH HOH . 
E 3 HOH A 32 333 46 HOH HOH . 
E 3 HOH A 33 334 52 HOH HOH . 
E 3 HOH A 34 335 53 HOH HOH . 
E 3 HOH A 35 336 55 HOH HOH . 
E 3 HOH A 36 337 58 HOH HOH . 
E 3 HOH A 37 338 60 HOH HOH . 
E 3 HOH A 38 339 61 HOH HOH . 
E 3 HOH A 39 340 62 HOH HOH . 
E 3 HOH A 40 341 64 HOH HOH . 
E 3 HOH A 41 342 65 HOH HOH . 
E 3 HOH A 42 343 66 HOH HOH . 
E 3 HOH A 43 344 67 HOH HOH . 
E 3 HOH A 44 345 68 HOH HOH . 
E 3 HOH A 45 346 74 HOH HOH . 
E 3 HOH A 46 347 75 HOH HOH . 
E 3 HOH A 47 348 76 HOH HOH . 
E 3 HOH A 48 349 79 HOH HOH . 
E 3 HOH A 49 350 80 HOH HOH . 
E 3 HOH A 50 351 86 HOH HOH . 
E 3 HOH A 51 352 92 HOH HOH . 
E 3 HOH A 52 353 93 HOH HOH . 
E 3 HOH A 53 354 95 HOH HOH . 
E 3 HOH A 54 355 96 HOH HOH . 
E 3 HOH A 55 356 97 HOH HOH . 
E 3 HOH A 56 357 98 HOH HOH . 
E 3 HOH A 57 358 99 HOH HOH . 
E 3 HOH A 58 359 100 HOH HOH . 
E 3 HOH A 59 360 104 HOH HOH . 
E 3 HOH A 60 361 105 HOH HOH . 
E 3 HOH A 61 362 106 HOH HOH . 
F 3 HOH B 1 303 2 HOH HOH . 
F 3 HOH B 2 304 3 HOH HOH . 
F 3 HOH B 3 305 11 HOH HOH . 
F 3 HOH B 4 306 12 HOH HOH . 
F 3 HOH B 5 307 24 HOH HOH . 
F 3 HOH B 6 308 25 HOH HOH . 
F 3 HOH B 7 309 26 HOH HOH . 
F 3 HOH B 8 310 27 HOH HOH . 
F 3 HOH B 9 311 33 HOH HOH . 
F 3 HOH B 10 312 34 HOH HOH . 
F 3 HOH B 11 313 35 HOH HOH . 
F 3 HOH B 12 314 40 HOH HOH . 
F 3 HOH B 13 315 44 HOH HOH . 
F 3 HOH B 14 316 45 HOH HOH . 
F 3 HOH B 15 317 47 HOH HOH . 
F 3 HOH B 16 318 48 HOH HOH . 
F 3 HOH B 17 319 49 HOH HOH . 
F 3 HOH B 18 320 50 HOH HOH . 
F 3 HOH B 19 321 51 HOH HOH . 
F 3 HOH B 20 322 54 HOH HOH . 
F 3 HOH B 21 323 56 HOH HOH . 
F 3 HOH B 22 324 57 HOH HOH . 
F 3 HOH B 23 325 59 HOH HOH . 
F 3 HOH B 24 326 63 HOH HOH . 
F 3 HOH B 25 327 69 HOH HOH . 
F 3 HOH B 26 328 70 HOH HOH . 
F 3 HOH B 27 329 71 HOH HOH . 
F 3 HOH B 28 330 72 HOH HOH . 
F 3 HOH B 29 331 73 HOH HOH . 
F 3 HOH B 30 332 77 HOH HOH . 
F 3 HOH B 31 333 78 HOH HOH . 
F 3 HOH B 32 334 81 HOH HOH . 
F 3 HOH B 33 335 82 HOH HOH . 
F 3 HOH B 34 336 83 HOH HOH . 
F 3 HOH B 35 337 84 HOH HOH . 
F 3 HOH B 36 338 85 HOH HOH . 
F 3 HOH B 37 339 87 HOH HOH . 
F 3 HOH B 38 340 88 HOH HOH . 
F 3 HOH B 39 341 89 HOH HOH . 
F 3 HOH B 40 342 90 HOH HOH . 
F 3 HOH B 41 343 91 HOH HOH . 
F 3 HOH B 42 344 94 HOH HOH . 
F 3 HOH B 43 345 101 HOH HOH . 
F 3 HOH B 44 346 102 HOH HOH . 
F 3 HOH B 45 347 103 HOH HOH . 
F 3 HOH B 46 348 107 HOH HOH . 
F 3 HOH B 47 349 108 HOH HOH . 
F 3 HOH B 48 350 109 HOH HOH . 
F 3 HOH B 49 351 110 HOH HOH . 
F 3 HOH B 50 352 111 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 UM3 . . . D 2 -2.978 25.955 12.116 1 27.34 ? N1 UM3 302 B 1 
HETATM 2 C C2 UM3 . . . D 2 -3.579 24.903 11.427 1 26.59 ? C2 UM3 302 B 1 
HETATM 3 N N3 UM3 . . . D 2 -2.707 24.069 10.777 1 23.72 ? N3 UM3 302 B 1 
HETATM 4 C C4 UM3 . . . D 2 -1.334 24.164 10.731 1 28.1 ? C4 UM3 302 B 1 
HETATM 5 C C5 UM3 . . . D 2 -0.785 25.256 11.478 1 30.04 ? C5 UM3 302 B 1 
HETATM 6 C C6 UM3 . . . D 2 -1.602 26.096 12.119 1 30.08 ? C6 UM3 302 B 1 
HETATM 7 O O2 UM3 . . . D 2 -4.788 24.707 11.407 1 25.82 ? O2 UM3 302 B 1 
HETATM 8 O O4 UM3 . . . D 2 -0.701 23.378 10.024 1 26.89 ? O4 UM3 302 B 1 
HETATM 9 C C1' UM3 . . . D 2 -3.843 26.919 12.825 1 30.42 ? C1' UM3 302 B 1 
HETATM 10 C C2' UM3 . . . D 2 -4.014 26.539 14.291 1 32.18 ? C2' UM3 302 B 1 
HETATM 11 C C3' UM3 . . . D 2 -3.805 27.827 15.069 1 33.53 ? C3' UM3 302 B 1 
HETATM 12 C C4' UM3 . . . D 2 -3.003 28.721 14.123 1 31.99 ? C4' UM3 302 B 1 
HETATM 13 O O3' UM3 . . . D 2 -5.048 28.417 15.463 1 31.27 ? O3' UM3 302 B 1 
HETATM 14 O O4' UM3 . . . D 2 -3.207 28.198 12.786 1 32.17 ? O4' UM3 302 B 1 
HETATM 15 C C5' UM3 . . . D 2 -1.523 28.763 14.435 1 29.53 ? C5' UM3 302 B 1 
HETATM 16 O O5' UM3 . . . D 2 -1.007 27.438 14.583 0 26.01 ? O5' UM3 302 B 1 
HETATM 17 P P UM3 . . . D 2 -5.707 28.008 16.874 0 22.91 ? P UM3 302 B 1 
HETATM 18 O O1P UM3 . . . D 2 -6.547 26.813 16.62 0 20.65 ? O1P UM3 302 B 1 
HETATM 19 O O2P UM3 . . . D 2 -6.314 29.212 17.5 0 21.03 ? O2P UM3 302 B 1 
HETATM 20 O O3P UM3 . . . D 2 -4.473 27.555 17.776 0 20.7 ? O3P UM3 302 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           323 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           20 
#