data_6BSV
#
_model_server_result.job_id            C-GFRmHeVggRRfTV3s47rQ 
_model_server_result.datetime_utc      '2024-11-02 03:37:59' 
_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          6bsv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":502}' 
#
_entry.id    6BSV 
#
_exptl.entry_id    6BSV 
_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            6BSV 
_cell.length_a            64.929 
_cell.length_b            94.549 
_cell.length_c            144.716 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6BSV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_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,E,F,G,H,I,J,K,L 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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 D N N 
? 3 H 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 47 A CYS 162 1_555 A SG CYS 269 A CYS 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf2 A SG CYS 266 A CYS 381 1_555 A SG CYS 280 A CYS 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf3 B SG CYS 47 B CYS 162 1_555 B SG CYS 269 B CYS 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf4 B SG CYS 266 B CYS 381 1_555 B SG CYS 280 B CYS 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
metalc ? metalc1 A OD2 ASP 112 A ASP 227 1_555 C MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? 
metalc ? metalc2 A OD1 ASP 114 A ASP 229 1_555 C MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? 
metalc ? metalc3 A NE2 HIS 262 A HIS 377 1_555 C MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
metalc ? metalc4 C MN MN . A MN 501 1_555 D O2B UDP . A UDP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? 
metalc ? metalc5 C MN MN . A MN 501 1_555 F O3 NO3 . A NO3 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.682 ? 
metalc ? metalc6 B OD2 ASP 112 B ASP 227 1_555 G MN MN . B MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? 
metalc ? metalc7 B OD1 ASP 114 B ASP 229 1_555 G MN MN . B MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? 
metalc ? metalc8 B OD2 ASP 114 B ASP 229 1_555 G MN MN . B MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? 
metalc ? metalc9 B NE2 HIS 262 B HIS 377 1_555 G MN MN . B MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? 
metalc ? metalc10 G MN MN . B MN 501 1_555 H O3B UDP . B UDP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? 
metalc ? metalc11 G MN MN . B MN 501 1_555 J O2 NO3 . B NO3 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? 
#
_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 380 n n 
N1 C6 UDP sing 381 n n 
N1 C1' UDP sing 382 n n 
C2 N3 UDP sing 383 n n 
C2 O2 UDP doub 384 n n 
N3 C4 UDP sing 385 n n 
N3 HN3 UDP sing 386 n n 
C4 C5 UDP sing 387 n n 
C4 O4 UDP doub 388 n n 
C5 C6 UDP doub 389 n n 
C5 H5 UDP sing 390 n n 
C6 H6 UDP sing 391 n n 
C1' C2' UDP sing 392 n n 
C1' O4' UDP sing 393 n n 
C1' H1' UDP sing 394 n n 
C2' O2' UDP sing 395 n n 
C2' C3' UDP sing 396 n n 
C2' H2' UDP sing 397 n n 
O2' HO2' UDP sing 398 n n 
C3' C4' UDP sing 399 n n 
C3' O3' UDP sing 400 n n 
C3' H3' UDP sing 401 n n 
C4' O4' UDP sing 402 n n 
C4' C5' UDP sing 403 n n 
C4' H4' UDP sing 404 n n 
O3' HO3' UDP sing 405 n n 
C5' O5' UDP sing 406 n n 
C5' "H5'1" UDP sing 407 n n 
C5' "H5'2" UDP sing 408 n n 
O5' PA UDP sing 409 n n 
PA O1A UDP doub 410 n n 
PA O2A UDP sing 411 n n 
PA O3A UDP sing 412 n n 
O2A HOA2 UDP sing 413 n n 
O3A PB UDP sing 414 n n 
PB O1B UDP doub 415 n n 
PB O2B UDP sing 416 n n 
PB O3B UDP sing 417 n n 
O2B HOB2 UDP sing 418 n n 
O3B HOB3 UDP sing 419 n n 
#
_atom_sites.entry_id                     6BSV 
_atom_sites.fract_transf_matrix[1][1]    0.015401 
_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]    0.010577 
_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]    0.00691 
_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 1 501 3 MN MN . 
D 3 UDP A 1 502 2 UDP UDP . 
E 4 TRS A 1 503 2 TRS TRS . 
F 5 NO3 A 1 504 2 NO3 NO3 . 
G 2 MN B 1 501 1 MN MN . 
H 3 UDP B 1 502 1 UDP UDP . 
I 4 TRS B 1 503 1 TRS TRS . 
J 5 NO3 B 1 504 1 NO3 NO3 . 
K 6 HOH A 1 601 94 HOH HOH . 
K 6 HOH A 2 602 4 HOH HOH . 
K 6 HOH A 3 603 54 HOH HOH . 
K 6 HOH A 4 604 78 HOH HOH . 
K 6 HOH A 5 605 26 HOH HOH . 
K 6 HOH A 6 606 11 HOH HOH . 
K 6 HOH A 7 607 32 HOH HOH . 
K 6 HOH A 8 608 48 HOH HOH . 
K 6 HOH A 9 609 44 HOH HOH . 
K 6 HOH A 10 610 69 HOH HOH . 
K 6 HOH A 11 611 3 HOH HOH . 
K 6 HOH A 12 612 1 HOH HOH . 
K 6 HOH A 13 613 53 HOH HOH . 
K 6 HOH A 14 614 97 HOH HOH . 
K 6 HOH A 15 615 13 HOH HOH . 
K 6 HOH A 16 616 28 HOH HOH . 
K 6 HOH A 17 617 9 HOH HOH . 
K 6 HOH A 18 618 82 HOH HOH . 
K 6 HOH A 19 619 67 HOH HOH . 
K 6 HOH A 20 620 74 HOH HOH . 
K 6 HOH A 21 621 61 HOH HOH . 
K 6 HOH A 22 622 83 HOH HOH . 
K 6 HOH A 23 623 85 HOH HOH . 
K 6 HOH A 24 624 46 HOH HOH . 
K 6 HOH A 25 625 16 HOH HOH . 
K 6 HOH A 26 626 77 HOH HOH . 
K 6 HOH A 27 627 49 HOH HOH . 
K 6 HOH A 28 628 66 HOH HOH . 
K 6 HOH A 29 629 31 HOH HOH . 
K 6 HOH A 30 630 101 HOH HOH . 
K 6 HOH A 31 631 43 HOH HOH . 
K 6 HOH A 32 632 87 HOH HOH . 
K 6 HOH A 33 633 86 HOH HOH . 
K 6 HOH A 34 634 38 HOH HOH . 
K 6 HOH A 35 635 80 HOH HOH . 
K 6 HOH A 36 636 36 HOH HOH . 
K 6 HOH A 37 637 37 HOH HOH . 
K 6 HOH A 38 638 33 HOH HOH . 
K 6 HOH A 39 639 29 HOH HOH . 
K 6 HOH A 40 640 23 HOH HOH . 
K 6 HOH A 41 641 34 HOH HOH . 
K 6 HOH A 42 642 41 HOH HOH . 
K 6 HOH A 43 643 98 HOH HOH . 
K 6 HOH A 44 644 39 HOH HOH . 
K 6 HOH A 45 645 73 HOH HOH . 
K 6 HOH A 46 646 84 HOH HOH . 
K 6 HOH A 47 647 100 HOH HOH . 
K 6 HOH A 48 648 70 HOH HOH . 
L 6 HOH B 1 601 17 HOH HOH . 
L 6 HOH B 2 602 79 HOH HOH . 
L 6 HOH B 3 603 64 HOH HOH . 
L 6 HOH B 4 604 45 HOH HOH . 
L 6 HOH B 5 605 47 HOH HOH . 
L 6 HOH B 6 606 24 HOH HOH . 
L 6 HOH B 7 607 2 HOH HOH . 
L 6 HOH B 8 608 60 HOH HOH . 
L 6 HOH B 9 609 27 HOH HOH . 
L 6 HOH B 10 610 7 HOH HOH . 
L 6 HOH B 11 611 35 HOH HOH . 
L 6 HOH B 12 612 6 HOH HOH . 
L 6 HOH B 13 613 92 HOH HOH . 
L 6 HOH B 14 614 21 HOH HOH . 
L 6 HOH B 15 615 76 HOH HOH . 
L 6 HOH B 16 616 8 HOH HOH . 
L 6 HOH B 17 617 10 HOH HOH . 
L 6 HOH B 18 618 22 HOH HOH . 
L 6 HOH B 19 619 71 HOH HOH . 
L 6 HOH B 20 620 93 HOH HOH . 
L 6 HOH B 21 621 96 HOH HOH . 
L 6 HOH B 22 622 89 HOH HOH . 
L 6 HOH B 23 623 59 HOH HOH . 
L 6 HOH B 24 624 58 HOH HOH . 
L 6 HOH B 25 625 56 HOH HOH . 
L 6 HOH B 26 626 19 HOH HOH . 
L 6 HOH B 27 627 68 HOH HOH . 
L 6 HOH B 28 628 63 HOH HOH . 
L 6 HOH B 29 629 15 HOH HOH . 
L 6 HOH B 30 630 20 HOH HOH . 
L 6 HOH B 31 631 55 HOH HOH . 
L 6 HOH B 32 632 62 HOH HOH . 
L 6 HOH B 33 633 5 HOH HOH . 
L 6 HOH B 34 634 12 HOH HOH . 
L 6 HOH B 35 635 95 HOH HOH . 
L 6 HOH B 36 636 18 HOH HOH . 
L 6 HOH B 37 637 81 HOH HOH . 
L 6 HOH B 38 638 57 HOH HOH . 
L 6 HOH B 39 639 52 HOH HOH . 
L 6 HOH B 40 640 42 HOH HOH . 
L 6 HOH B 41 641 14 HOH HOH . 
L 6 HOH B 42 642 99 HOH HOH . 
L 6 HOH B 43 643 75 HOH HOH . 
L 6 HOH B 44 644 88 HOH HOH . 
L 6 HOH B 45 645 25 HOH HOH . 
L 6 HOH B 46 646 30 HOH HOH . 
L 6 HOH B 47 647 51 HOH HOH . 
L 6 HOH B 48 648 90 HOH HOH . 
L 6 HOH B 49 649 50 HOH HOH . 
L 6 HOH B 50 650 40 HOH HOH . 
L 6 HOH B 51 651 65 HOH HOH . 
L 6 HOH B 52 652 91 HOH HOH . 
L 6 HOH B 53 653 72 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 . . . H 3 -32.459 14.734 -26.717 1 48.05 ? N1 UDP 502 B 1 
HETATM 2 C C2 UDP . . . H 3 -31.783 13.422 -26.545 1 46.46 ? C2 UDP 502 B 1 
HETATM 3 N N3 UDP . . . H 3 -32.578 12.147 -26.607 1 55.35 ? N3 UDP 502 B 1 
HETATM 4 C C4 UDP . . . H 3 -34.006 12.199 -26.831 1 49.36 ? C4 UDP 502 B 1 
HETATM 5 C C5 UDP . . . H 3 -34.69 13.522 -27.002 1 48.03 ? C5 UDP 502 B 1 
HETATM 6 C C6 UDP . . . H 3 -33.902 14.781 -26.94 1 52.15 ? C6 UDP 502 B 1 
HETATM 7 O O2 UDP . . . H 3 -30.625 13.384 -26.363 1 48.73 ? O2 UDP 502 B 1 
HETATM 8 O O4 UDP . . . H 3 -34.636 11.188 -26.879 1 59.37 ? O4 UDP 502 B 1 
HETATM 9 C C1' UDP . . . H 3 -31.747 15.852 -26.655 1 46.81 ? C1' UDP 502 B 1 
HETATM 10 C C2' UDP . . . H 3 -31.698 16.579 -28.02 1 44.8 ? C2' UDP 502 B 1 
HETATM 11 O O2' UDP . . . H 3 -30.345 17.115 -28.255 1 36.79 ? O2' UDP 502 B 1 
HETATM 12 C C3' UDP . . . H 3 -32.576 17.574 -27.904 1 44.6 ? C3' UDP 502 B 1 
HETATM 13 C C4' UDP . . . H 3 -32.499 18.004 -26.327 1 49.14 ? C4' UDP 502 B 1 
HETATM 14 O O4' UDP . . . H 3 -32.426 16.877 -25.666 1 44.99 ? O4' UDP 502 B 1 
HETATM 15 O O3' UDP . . . H 3 -32.224 18.659 -28.765 1 35.33 ? O3' UDP 502 B 1 
HETATM 16 C C5' UDP . . . H 3 -33.734 18.746 -25.92 1 52.67 ? C5' UDP 502 B 1 
HETATM 17 O O5' UDP . . . H 3 -34.849 17.915 -26.103 1 64.23 ? O5' UDP 502 B 1 
HETATM 18 P PA UDP . . . H 3 -36.217 18.563 -26.794 1 72.96 ? PA UDP 502 B 1 
HETATM 19 O O1A UDP . . . H 3 -37.379 17.612 -26.607 1 63.07 -1 O1A UDP 502 B 1 
HETATM 20 O O2A UDP . . . H 3 -36.521 19.896 -26.141 1 60.93 ? O2A UDP 502 B 1 
HETATM 21 O O3A UDP . . . H 3 -35.954 18.791 -28.415 1 60.23 ? O3A UDP 502 B 1 
HETATM 22 P PB UDP . . . H 3 -35.451 20.222 -29.082 1 53.72 ? PB UDP 502 B 1 
HETATM 23 O O1B UDP . . . H 3 -34.621 19.959 -30.332 1 52.58 -1 O1B UDP 502 B 1 
HETATM 24 O O2B UDP . . . H 3 -36.667 21.026 -29.491 1 59.82 ? O2B UDP 502 B 1 
HETATM 25 O O3B UDP . . . H 3 -34.625 20.993 -28.07 1 42.65 ? O3B UDP 502 B 1 
HETATM 26 H HN3 UDP . . . H 3 -32.185 11.389 -26.509 1 66.52 ? HN3 UDP 502 B 1 
HETATM 27 H H5 UDP . . . H 3 -35.608 13.556 -27.146 1 57.74 ? H5 UDP 502 B 1 
HETATM 28 H H6 UDP . . . H 3 -34.329 15.601 -27.046 1 62.69 ? H6 UDP 502 B 1 
HETATM 29 H H1' UDP . . . H 3 -30.845 15.657 -26.356 1 56.27 ? H1' UDP 502 B 1 
HETATM 30 H H2' UDP . . . H 3 -31.961 15.978 -28.735 1 53.86 ? H2' UDP 502 B 1 
HETATM 31 H HO2' UDP . . . H 3 -29.768 16.567 -27.957 1 44.25 ? HO2' UDP 502 B 1 
HETATM 32 H H3' UDP . . . H 3 -33.467 17.253 -28.115 1 53.62 ? H3' UDP 502 B 1 
HETATM 33 H H4' UDP . . . H 3 -31.707 18.54 -26.163 1 59.07 ? H4' UDP 502 B 1 
HETATM 34 H "H5'1" UDP . . . H 3 -33.828 19.539 -26.471 1 63.3 ? "H5'1" UDP 502 B 1 
HETATM 35 H "H5'2" UDP . . . H 3 -33.668 19.002 -24.986 1 63.3 ? "H5'2" UDP 502 B 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    33 
_model_server_stats.query_time_ms           314 
_model_server_stats.encode_time_ms          14 
_model_server_stats.element_count           35 
#