data_2FFV
#
_model_server_result.job_id            4FEhT6XpEPzzcvc3hQsouA 
_model_server_result.datetime_utc      '2024-11-28 02:40:35' 
_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          2ffv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":9601}' 
#
_entry.id    2FFV 
#
_exptl.entry_id    2FFV 
_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         90 
_cell.entry_id            2FFV 
_cell.length_a            153.228 
_cell.length_b            153.228 
_cell.length_c            110.144 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2FFV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
PISA,PQS tetrameric 4 software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D 1 1 
B,E,F 2 1 
A,B,C,D,E,F 3 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' 8_554 -y,-x,-z-1/2 0 -1 0 -1 0 0 0 0 -1 0 0 -55.072 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 F 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 56 A CYS 126 1_555 A SG CYS 284 A CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf2 A SG CYS 275 A CYS 345 1_555 A SG CYS 353 A CYS 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf3 A SG CYS 386 A CYS 456 1_555 A SG CYS 403 A CYS 473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf4 A SG CYS 426 A CYS 496 1_555 A SG CYS 443 A CYS 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf5 A SG CYS 469 A CYS 539 1_555 A SG CYS 485 A CYS 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf6 B SG CYS 56 B CYS 126 1_555 B SG CYS 284 B CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf7 B SG CYS 275 B CYS 345 1_555 B SG CYS 353 B CYS 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf8 B SG CYS 386 B CYS 456 1_555 B SG CYS 403 B CYS 473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf9 B SG CYS 426 B CYS 496 1_555 B SG CYS 443 B CYS 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf10 B SG CYS 469 B CYS 539 1_555 B SG CYS 485 B CYS 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
metalc ? metalc1 A OD2 ASP 154 A ASP 224 1_555 C MN MN . A MN 5600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? 
metalc ? metalc2 A NE2 HIS 156 A HIS 226 1_555 C MN MN . A MN 5600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? 
metalc ? metalc3 A NE2 HIS 289 A HIS 359 1_555 C MN MN . A MN 5600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? 
metalc ? metalc4 C MN MN . A MN 5600 1_555 D O2A UDP . A UDP 5601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? 
metalc ? metalc5 C MN MN . A MN 5600 1_555 D O1B UDP . A UDP 5601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? 
metalc ? metalc6 B OD2 ASP 154 B ASP 224 1_555 E MN MN . B MN 9600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
metalc ? metalc7 B NE2 HIS 156 B HIS 226 1_555 E MN MN . B MN 9600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? 
metalc ? metalc8 B NE2 HIS 289 B HIS 359 1_555 E MN MN . B MN 9600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? 
metalc ? metalc9 E MN MN . B MN 9600 1_555 F O2A UDP . B UDP 9601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? 
metalc ? metalc10 E MN MN . B MN 9600 1_555 F O1B UDP . B UDP 9601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
#
_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 356 n n 
N1 C6 UDP sing 357 n n 
N1 C1' UDP sing 358 n n 
C2 N3 UDP sing 359 n n 
C2 O2 UDP doub 360 n n 
N3 C4 UDP sing 361 n n 
N3 HN3 UDP sing 362 n n 
C4 C5 UDP sing 363 n n 
C4 O4 UDP doub 364 n n 
C5 C6 UDP doub 365 n n 
C5 H5 UDP sing 366 n n 
C6 H6 UDP sing 367 n n 
C1' C2' UDP sing 368 n n 
C1' O4' UDP sing 369 n n 
C1' H1' UDP sing 370 n n 
C2' O2' UDP sing 371 n n 
C2' C3' UDP sing 372 n n 
C2' H2' UDP sing 373 n n 
O2' HO2' UDP sing 374 n n 
C3' C4' UDP sing 375 n n 
C3' O3' UDP sing 376 n n 
C3' H3' UDP sing 377 n n 
C4' O4' UDP sing 378 n n 
C4' C5' UDP sing 379 n n 
C4' H4' UDP sing 380 n n 
O3' HO3' UDP sing 381 n n 
C5' O5' UDP sing 382 n n 
C5' "H5'1" UDP sing 383 n n 
C5' "H5'2" UDP sing 384 n n 
O5' PA UDP sing 385 n n 
PA O1A UDP doub 386 n n 
PA O2A UDP sing 387 n n 
PA O3A UDP sing 388 n n 
O2A HOA2 UDP sing 389 n n 
O3A PB UDP sing 390 n n 
PB O1B UDP doub 391 n n 
PB O2B UDP sing 392 n n 
PB O3B UDP sing 393 n n 
O2B HOB2 UDP sing 394 n n 
O3B HOB3 UDP sing 395 n n 
#
_atom_sites.entry_id                     2FFV 
_atom_sites.fract_transf_matrix[1][1]    0.006526 
_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]    0.006526 
_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]    0.009079 
_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 MN A 1 5600 5600 MN MN . 
D 3 UDP A 1 5601 5601 UDP UDP . 
E 2 MN B 1 9600 9600 MN MN . 
F 3 UDP B 1 9601 9601 UDP UDP . 
#
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 . . . F 3 41.314 -55.26 7.123 1 67.39 ? N1 UDP 9601 B 1 
HETATM 2 C C2 UDP . . . F 3 42.057 -56.398 7.621 1 67.68 ? C2 UDP 9601 B 1 
HETATM 3 N N3 UDP . . . F 3 41.478 -57.268 8.547 1 67.62 ? N3 UDP 9601 B 1 
HETATM 4 C C4 UDP . . . F 3 40.156 -57.119 9.045 1 67.43 ? C4 UDP 9601 B 1 
HETATM 5 C C5 UDP . . . F 3 39.247 -55.977 8.618 1 67.57 ? C5 UDP 9601 B 1 
HETATM 6 C C6 UDP . . . F 3 39.896 -55.019 7.597 1 67.31 ? C6 UDP 9601 B 1 
HETATM 7 O O2 UDP . . . F 3 43.225 -56.626 7.254 1 68.72 ? O2 UDP 9601 B 1 
HETATM 8 O O4 UDP . . . F 3 39.75 -57.927 9.84 1 67.17 ? O4 UDP 9601 B 1 
HETATM 9 C C1' UDP . . . F 3 42.003 -54.362 6.127 1 67.64 ? C1' UDP 9601 B 1 
HETATM 10 C C2' UDP . . . F 3 41.686 -54.919 4.742 1 68.23 ? C2' UDP 9601 B 1 
HETATM 11 O O2' UDP . . . F 3 42.366 -55.964 4.06 1 68.69 ? O2' UDP 9601 B 1 
HETATM 12 C C3' UDP . . . F 3 42.074 -53.682 3.983 1 68.03 ? C3' UDP 9601 B 1 
HETATM 13 C C4' UDP . . . F 3 41.414 -52.645 4.662 1 67.33 ? C4' UDP 9601 B 1 
HETATM 14 O O4' UDP . . . F 3 41.361 -53.082 6.022 1 67.29 ? O4' UDP 9601 B 1 
HETATM 15 O O3' UDP . . . F 3 43.46 -53.342 3.885 1 68.7 ? O3' UDP 9601 B 1 
HETATM 16 C C5' UDP . . . F 3 40.041 -52.176 4.097 1 66.39 ? C5' UDP 9601 B 1 
HETATM 17 O O5' UDP . . . F 3 39.066 -52.612 5.056 1 64.12 ? O5' UDP 9601 B 1 
HETATM 18 P PA UDP . . . F 3 37.755 -53.301 4.58 1 61.68 ? PA UDP 9601 B 1 
HETATM 19 O O1A UDP . . . F 3 37.748 -54.714 4.771 1 62.66 ? O1A UDP 9601 B 1 
HETATM 20 O O2A UDP . . . F 3 36.504 -52.541 5.16 1 60.81 ? O2A UDP 9601 B 1 
HETATM 21 O O3A UDP . . . F 3 37.746 -53.042 3.011 1 60.82 ? O3A UDP 9601 B 1 
HETATM 22 P PB UDP . . . F 3 36.99 -51.857 2.226 1 58.67 ? PB UDP 9601 B 1 
HETATM 23 O O1B UDP . . . F 3 35.504 -51.878 2.554 1 59.32 ? O1B UDP 9601 B 1 
HETATM 24 O O2B UDP . . . F 3 37.316 -52.078 0.733 1 59.63 ? O2B UDP 9601 B 1 
HETATM 25 O O3B UDP . . . F 3 37.545 -50.371 2.461 1 59.17 ? O3B UDP 9601 B 1 
#
_model_server_stats.io_time_ms              65 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           278 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#