data_9H6L
#
_model_server_result.job_id            Aa67YNQ_1aGFI6qqnzu6eg 
_model_server_result.datetime_utc      '2025-07-21 17:07:47' 
_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          9h6l 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":601}' 
#
_entry.id    9H6L 
#
_exptl.entry_id    9H6L 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          3 
_entity.src_method                  man 
_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          94.83 
_cell.angle_gamma         90 
_cell.entry_id            9H6L 
_cell.length_a            60.183 
_cell.length_b            133.527 
_cell.length_c            86.922 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9H6L 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_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 E N N 
? 3 H N N 
#
_pdbx_entity_branch.entity_id    2 
_pdbx_entity_branch.type         oligosaccharide 
#
loop_
_pdbx_entity_branch_link.link_id
_pdbx_entity_branch_link.details
_pdbx_entity_branch_link.entity_id
_pdbx_entity_branch_link.entity_branch_list_num_1
_pdbx_entity_branch_link.entity_branch_list_num_2
_pdbx_entity_branch_link.comp_id_1
_pdbx_entity_branch_link.comp_id_2
_pdbx_entity_branch_link.atom_id_1
_pdbx_entity_branch_link.leaving_atom_id_1
_pdbx_entity_branch_link.atom_stereo_config_1
_pdbx_entity_branch_link.atom_id_2
_pdbx_entity_branch_link.leaving_atom_id_2
_pdbx_entity_branch_link.atom_stereo_config_2
_pdbx_entity_branch_link.value_order
1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 
#
loop_
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.hetero
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.auth_mon_id
2 n C NAG 1 C 1 NAG A 536 NAG 
2 n C NAG 2 C 2 NAG A 537 NAG 
2 n C BMA 3 C 3 BMA A 702 BMA 
2 n D NAG 1 D 1 NAG B 536 NAG 
2 n D NAG 2 D 2 NAG B 702 NAG 
2 n D BMA 3 D 3 BMA B 703 BMA 
#
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 46 A CYS 80 1_555 A SG CYS 378 A CYS 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
disulf ? disulf2 A SG CYS 48 A CYS 82 1_555 A SG CYS 495 A CYS 529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? 
disulf ? disulf3 A SG CYS 395 A CYS 429 1_555 A SG CYS 442 A CYS 476 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? 
disulf ? disulf4 B SG CYS 46 B CYS 80 1_555 B SG CYS 378 B CYS 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? 
disulf ? disulf5 B SG CYS 48 B CYS 82 1_555 B SG CYS 495 B CYS 529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? 
disulf ? disulf6 B SG CYS 395 B CYS 429 1_555 B SG CYS 442 B CYS 476 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
covale ? covale1 A ND2 ASN 240 A ASN 274 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? 
covale ? covale2 B ND2 ASN 240 B ASN 274 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? 
covale ? covale3 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.392 ? 
covale ? covale4 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.392 ? 
covale ? covale5 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.389 ? 
covale ? covale6 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.395 ? 
metalc ? metalc1 A OD2 ASP 324 A ASP 358 1_555 F MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.759 ? 
metalc ? metalc2 A NE2 HIS 449 A HIS 483 1_555 F MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
metalc ? metalc3 E O2A UDP . A UDP 601 1_555 F MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.81 ? 
metalc ? metalc4 E O2B UDP . A UDP 601 1_555 F MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.772 ? 
metalc ? metalc5 B OD2 ASP 324 B ASP 358 1_555 I MN MN . B MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.796 ? 
metalc ? metalc6 B NE2 HIS 449 B HIS 483 1_555 I MN MN . B MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.876 ? 
metalc ? metalc7 H O2A UDP . B UDP 601 1_555 I MN MN . B MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.815 ? 
metalc ? metalc8 H O3B UDP . B UDP 601 1_555 I MN MN . B MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.792 ? 
#
_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 419 n n 
N1 C6 UDP sing 420 n n 
N1 C1' UDP sing 421 n n 
C2 N3 UDP sing 422 n n 
C2 O2 UDP doub 423 n n 
N3 C4 UDP sing 424 n n 
N3 HN3 UDP sing 425 n n 
C4 C5 UDP sing 426 n n 
C4 O4 UDP doub 427 n n 
C5 C6 UDP doub 428 n n 
C5 H5 UDP sing 429 n n 
C6 H6 UDP sing 430 n n 
C1' C2' UDP sing 431 n n 
C1' O4' UDP sing 432 n n 
C1' H1' UDP sing 433 n n 
C2' O2' UDP sing 434 n n 
C2' C3' UDP sing 435 n n 
C2' H2' UDP sing 436 n n 
O2' HO2' UDP sing 437 n n 
C3' C4' UDP sing 438 n n 
C3' O3' UDP sing 439 n n 
C3' H3' UDP sing 440 n n 
C4' O4' UDP sing 441 n n 
C4' C5' UDP sing 442 n n 
C4' H4' UDP sing 443 n n 
O3' HO3' UDP sing 444 n n 
C5' O5' UDP sing 445 n n 
C5' "H5'1" UDP sing 446 n n 
C5' "H5'2" UDP sing 447 n n 
O5' PA UDP sing 448 n n 
PA O1A UDP doub 449 n n 
PA O2A UDP sing 450 n n 
PA O3A UDP sing 451 n n 
O2A HOA2 UDP sing 452 n n 
O3A PB UDP sing 453 n n 
PB O1B UDP doub 454 n n 
PB O2B UDP sing 455 n n 
PB O3B UDP sing 456 n n 
O2B HOB2 UDP sing 457 n n 
O3B HOB3 UDP sing 458 n n 
#
_atom_sites.entry_id                     9H6L 
_atom_sites.fract_transf_matrix[1][1]    0.016616 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001404 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007489 
_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]    0.011546 
_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 3 UDP A 1 601 601 UDP UDP . 
F 4 MN A 1 602 602 MN MN . 
G 5 ACY A 1 603 701 ACY ACY . 
H 3 UDP B 1 601 601 UDP UDP . 
I 4 MN B 1 602 602 MN MN . 
J 5 ACY B 1 603 701 ACY ACY . 
K 6 HOH A 1 701 15 HOH HOH . 
K 6 HOH A 2 702 19 HOH HOH . 
K 6 HOH A 3 703 3 HOH HOH . 
K 6 HOH A 4 704 9 HOH HOH . 
K 6 HOH A 5 705 2 HOH HOH . 
K 6 HOH A 6 706 27 HOH HOH . 
K 6 HOH A 7 707 18 HOH HOH . 
K 6 HOH A 8 708 12 HOH HOH . 
K 6 HOH A 9 709 16 HOH HOH . 
K 6 HOH A 10 710 11 HOH HOH . 
K 6 HOH A 11 711 8 HOH HOH . 
K 6 HOH A 12 712 20 HOH HOH . 
K 6 HOH A 13 713 17 HOH HOH . 
L 6 HOH B 1 701 21 HOH HOH . 
L 6 HOH B 2 702 13 HOH HOH . 
L 6 HOH B 3 703 14 HOH HOH . 
L 6 HOH B 4 704 22 HOH HOH . 
L 6 HOH B 5 705 26 HOH HOH . 
L 6 HOH B 6 706 10 HOH HOH . 
L 6 HOH B 7 707 25 HOH HOH . 
L 6 HOH B 8 708 4 HOH HOH . 
L 6 HOH B 9 709 24 HOH HOH . 
L 6 HOH B 10 710 7 HOH HOH . 
L 6 HOH B 11 711 23 HOH HOH . 
L 6 HOH B 12 712 5 HOH HOH . 
L 6 HOH B 13 713 6 HOH HOH . 
L 6 HOH B 14 714 1 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 -6.162 18.009 52.93 1 71.54 ? N1 UDP 601 B 1 
HETATM 2 C C2 UDP . . . H 3 -4.822 17.769 53.265 1 71.61 ? C2 UDP 601 B 1 
HETATM 3 N N3 UDP . . . H 3 -4.608 17.084 54.449 1 69.94 ? N3 UDP 601 B 1 
HETATM 4 C C4 UDP . . . H 3 -5.575 16.637 55.334 1 83.25 ? C4 UDP 601 B 1 
HETATM 5 C C5 UDP . . . H 3 -6.928 16.951 54.94 1 91.17 ? C5 UDP 601 B 1 
HETATM 6 C C6 UDP . . . H 3 -7.171 17.612 53.788 1 77.55 ? C6 UDP 601 B 1 
HETATM 7 O O2 UDP . . . H 3 -3.881 18.113 52.561 1 63.84 ? O2 UDP 601 B 1 
HETATM 8 O O4 UDP . . . H 3 -5.232 16.03 56.355 1 88.6 ? O4 UDP 601 B 1 
HETATM 9 C C1' UDP . . . H 3 -6.456 18.762 51.661 1 71.95 ? C1' UDP 601 B 1 
HETATM 10 C C2' UDP . . . H 3 -7.464 18.099 50.707 1 77.45 ? C2' UDP 601 B 1 
HETATM 11 O O2' UDP . . . H 3 -7.078 18.061 49.345 1 73.72 ? O2' UDP 601 B 1 
HETATM 12 C C3' UDP . . . H 3 -8.761 18.917 50.912 1 80.45 ? C3' UDP 601 B 1 
HETATM 13 C C4' UDP . . . H 3 -8.279 20.261 51.471 1 73.74 ? C4' UDP 601 B 1 
HETATM 14 O O4' UDP . . . H 3 -6.938 20.057 51.972 1 71.54 ? O4' UDP 601 B 1 
HETATM 15 O O3' UDP . . . H 3 -9.715 19.122 49.859 1 76.4 ? O3' UDP 601 B 1 
HETATM 16 C C5' UDP . . . H 3 -9.124 20.779 52.601 1 75.91 ? C5' UDP 601 B 1 
HETATM 17 O O5' UDP . . . H 3 -8.826 22.174 52.788 1 72.17 ? O5' UDP 601 B 1 
HETATM 18 P PA UDP . . . H 3 -9.653 22.99 53.881 1 72.1 ? PA UDP 601 B 1 
HETATM 19 O O1A UDP . . . H 3 -9.161 24.395 53.843 1 77.71 ? O1A UDP 601 B 1 
HETATM 20 O O2A UDP . . . H 3 -11.143 22.709 53.79 1 91.83 ? O2A UDP 601 B 1 
HETATM 21 O O3A UDP . . . H 3 -9.135 22.286 55.247 1 74.23 ? O3A UDP 601 B 1 
HETATM 22 P PB UDP . . . H 3 -9.81 21.191 56.245 1 84.01 ? PB UDP 601 B 1 
HETATM 23 O O1B UDP . . . H 3 -9.907 21.915 57.566 1 99.37 ? O1B UDP 601 B 1 
HETATM 24 O O2B UDP . . . H 3 -8.992 19.902 56.365 1 86.18 ? O2B UDP 601 B 1 
HETATM 25 O O3B UDP . . . H 3 -11.2 20.969 55.548 1 100.61 ? O3B UDP 601 B 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           304 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#