data_7VTE
#
_model_server_result.job_id            ky6ykqcoTsG2wrumYKgOLA 
_model_server_result.datetime_utc      '2024-12-09 12:12:53' 
_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          7vte 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":402}' 
#
_entry.id    7VTE 
#
_exptl.entry_id    7VTE 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              244.201 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            URIDINE 
_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         120 
_cell.entry_id            7VTE 
_cell.length_a            185.689 
_cell.length_b            185.689 
_cell.length_c            50.754 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7VTE 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        143 
_symmetry.space_group_name_Hall    'P 3' 
_symmetry.space_group_name_H-M     'P 3' 
#
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
? 3 F N N 
? 3 H N N 
? 3 J N N 
? 3 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 A OD1 ASN 250 A ASN 250 1_555 E K K . A K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? 
metalc ? metalc2 A O THR 252 A THR 252 1_555 E K K . A K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? 
metalc ? metalc3 A O ALA 286 A ALA 286 1_555 E K K . A K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? 
metalc ? metalc4 A O CYS 289 A CYS 289 1_555 E K K . A K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.04 ? 
metalc ? metalc5 A O TYR 291 A TYR 291 1_555 E K K . A K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? 
metalc ? metalc6 B O ASN 250 B ASN 250 1_555 G K K . B K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.986 ? 
metalc ? metalc7 B OD1 ASN 250 B ASN 250 1_555 G K K . B K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? 
metalc ? metalc8 B O THR 252 B THR 252 1_555 G K K . B K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.697 ? 
metalc ? metalc9 B O ALA 286 B ALA 286 1_555 G K K . B K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? 
metalc ? metalc10 B O CYS 289 B CYS 289 1_555 G K K . B K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? 
metalc ? metalc11 B O TYR 291 B TYR 291 1_555 G K K . B K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.01 ? 
metalc ? metalc12 C OD1 ASN 250 C ASN 250 1_555 I K K . C K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.695 ? 
metalc ? metalc13 C O THR 252 C THR 252 1_555 I K K . C K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? 
metalc ? metalc14 C O ALA 286 C ALA 286 1_555 I K K . C K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? 
metalc ? metalc15 C O CYS 289 C CYS 289 1_555 I K K . C K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.226 ? 
metalc ? metalc16 C O TYR 291 C TYR 291 1_555 I K K . C K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.567 ? 
metalc ? metalc17 D OD1 ASN 250 D ASN 250 1_555 K K K . D K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.744 ? 
metalc ? metalc18 D O THR 252 D THR 252 1_555 K K K . D K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? 
metalc ? metalc19 D O ALA 286 D ALA 286 1_555 K K K . D K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.646 ? 
metalc ? metalc20 D O CYS 289 D CYS 289 1_555 K K K . D K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.188 ? 
metalc ? metalc21 D O TYR 291 D TYR 291 1_555 K K K . D K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.612 ? 
#
_chem_comp.formula           'C9 H12 N2 O6' 
_chem_comp.formula_weight    244.201 
_chem_comp.id                URI 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              URIDINE 
_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 URI sing 358 n n 
N1 C6 URI sing 359 n n 
N1 C1' URI sing 360 n n 
C2 N3 URI sing 361 n n 
C2 O2 URI doub 362 n n 
N3 C4 URI sing 363 n n 
N3 H3 URI sing 364 n n 
C4 C5 URI sing 365 n n 
C4 O4 URI doub 366 n n 
C5 C6 URI doub 367 n n 
C5 H5 URI sing 368 n n 
C6 H6 URI sing 369 n n 
C1' C2' URI sing 370 n n 
C1' O4' URI sing 371 n n 
C1' H1' URI sing 372 n n 
C2' C3' URI sing 373 n n 
C2' O2' URI sing 374 n n 
C2' H2' URI sing 375 n n 
C3' C4' URI sing 376 n n 
C3' O3' URI sing 377 n n 
C3' H3' URI sing 378 n n 
C4' O4' URI sing 379 n n 
C4' C5' URI sing 380 n n 
C4' H4' URI sing 381 n n 
O2' HO2' URI sing 382 n n 
O3' HO3' URI sing 383 n n 
C5' O5' URI sing 384 n n 
C5' "H5'1" URI sing 385 n n 
C5' "H5'2" URI sing 386 n n 
O5' HO5' URI sing 387 n n 
#
_atom_sites.entry_id                     7VTE 
_atom_sites.fract_transf_matrix[1][1]    0.005385 
_atom_sites.fract_transf_matrix[1][2]    0.003109 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006218 
_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]    0.019703 
_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 K A 1 401 403 K K . 
F 3 URI A 1 402 402 URI URI . 
G 2 K B 1 401 403 K K . 
H 3 URI B 1 402 402 URI URI . 
I 2 K C 1 401 403 K K . 
J 3 URI C 1 402 402 URI URI . 
K 2 K D 1 401 403 K K . 
L 3 URI D 1 402 402 URI URI . 
M 4 HOH A 1 501 10 HOH HOH . 
M 4 HOH A 2 502 31 HOH HOH . 
M 4 HOH A 3 503 1 HOH HOH . 
M 4 HOH A 4 504 11 HOH HOH . 
M 4 HOH A 5 505 20 HOH HOH . 
M 4 HOH A 6 506 21 HOH HOH . 
M 4 HOH A 7 507 6 HOH HOH . 
M 4 HOH A 8 508 15 HOH HOH . 
M 4 HOH A 9 509 33 HOH HOH . 
M 4 HOH A 10 510 18 HOH HOH . 
M 4 HOH A 11 511 29 HOH HOH . 
N 4 HOH B 1 501 14 HOH HOH . 
N 4 HOH B 2 502 9 HOH HOH . 
N 4 HOH B 3 503 37 HOH HOH . 
N 4 HOH B 4 504 26 HOH HOH . 
N 4 HOH B 5 505 5 HOH HOH . 
N 4 HOH B 6 506 22 HOH HOH . 
N 4 HOH B 7 507 7 HOH HOH . 
N 4 HOH B 8 508 24 HOH HOH . 
O 4 HOH C 1 501 23 HOH HOH . 
O 4 HOH C 2 502 36 HOH HOH . 
O 4 HOH C 3 503 25 HOH HOH . 
O 4 HOH C 4 504 32 HOH HOH . 
O 4 HOH C 5 505 16 HOH HOH . 
O 4 HOH C 6 506 4 HOH HOH . 
O 4 HOH C 7 507 12 HOH HOH . 
O 4 HOH C 8 508 3 HOH HOH . 
O 4 HOH C 9 509 27 HOH HOH . 
O 4 HOH C 10 510 34 HOH HOH . 
P 4 HOH D 1 501 38 HOH HOH . 
P 4 HOH D 2 502 19 HOH HOH . 
P 4 HOH D 3 503 13 HOH HOH . 
P 4 HOH D 4 504 2 HOH HOH . 
P 4 HOH D 5 505 30 HOH HOH . 
P 4 HOH D 6 506 17 HOH HOH . 
P 4 HOH D 7 507 8 HOH HOH . 
P 4 HOH D 8 508 28 HOH HOH . 
P 4 HOH D 9 509 35 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 URI . . . J 3 32.258 2.544 30.351 1 114.06 ? N1 URI 402 C 1 
HETATM 2 C C2 URI . . . J 3 33.305 2.076 29.571 1 104.49 ? C2 URI 402 C 1 
HETATM 3 N N3 URI . . . J 3 32.974 1.135 28.624 1 108.15 ? N3 URI 402 C 1 
HETATM 4 C C4 URI . . . J 3 31.716 0.623 28.377 1 112.18 ? C4 URI 402 C 1 
HETATM 5 C C5 URI . . . J 3 30.682 1.164 29.219 1 122.44 ? C5 URI 402 C 1 
HETATM 6 C C6 URI . . . J 3 30.973 2.082 30.151 1 123.24 ? C6 URI 402 C 1 
HETATM 7 O O2 URI . . . J 3 34.451 2.466 29.716 1 95.79 ? O2 URI 402 C 1 
HETATM 8 O O4 URI . . . J 3 31.578 -0.221 27.484 1 100.46 ? O4 URI 402 C 1 
HETATM 9 C C1' URI . . . J 3 32.585 3.559 31.371 1 97.69 ? C1' URI 402 C 1 
HETATM 10 C C2' URI . . . J 3 31.565 4.692 31.476 1 94.05 ? C2' URI 402 C 1 
HETATM 11 C C3' URI . . . J 3 31.708 5.132 32.935 1 98.21 ? C3' URI 402 C 1 
HETATM 12 C C4' URI . . . J 3 32.138 3.852 33.659 1 99.36 ? C4' URI 402 C 1 
HETATM 13 O O2' URI . . . J 3 31.863 5.716 30.547 1 65.34 ? O2' URI 402 C 1 
HETATM 14 O O3' URI . . . J 3 32.748 6.104 33.024 1 93.46 ? O3' URI 402 C 1 
HETATM 15 O O4' URI . . . J 3 32.614 2.933 32.638 1 85.2 ? O4' URI 402 C 1 
HETATM 16 C C5' URI . . . J 3 31.075 3.168 34.485 1 110.77 ? C5' URI 402 C 1 
HETATM 17 O O5' URI . . . J 3 31.643 2.189 35.353 1 118.64 ? O5' URI 402 C 1 
#
_model_server_stats.io_time_ms              123 
_model_server_stats.parse_time_ms           38 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           17 
#