data_8KB7
#
_model_server_result.job_id            phQdt9MX-j8IW8DPzVOJKg 
_model_server_result.datetime_utc      '2024-11-16 11:44:31' 
_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          8kb7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":601}' 
#
_entry.id    8KB7 
#
_exptl.entry_id    8KB7 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE" 
_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         90 
_cell.entry_id            8KB7 
_cell.length_a            145.019 
_cell.length_b            150.002 
_cell.length_c            191.481 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8KB7 
_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        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,M,N,O,P,Q,R,S,T,U,V 
_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
? 2 E N N 
? 2 J N N 
? 2 N N N 
? 2 S 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 69 1_555 A SG CYS 57 A CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf2 A SG CYS 63 A CYS 85 1_555 A SG CYS 206 A CYS 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 
disulf ? disulf3 A SG CYS 414 A CYS 436 1_555 A SG CYS 415 A CYS 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? 
disulf ? disulf4 A SG CYS 468 A CYS 490 1_555 A SG CYS 556 A CYS 578 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
disulf ? disulf5 B SG CYS 47 B CYS 69 1_555 B SG CYS 57 B CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf6 B SG CYS 63 B CYS 85 1_555 B SG CYS 206 B CYS 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 
disulf ? disulf7 B SG CYS 414 B CYS 436 1_555 B SG CYS 415 B CYS 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
disulf ? disulf8 B SG CYS 468 B CYS 490 1_555 B SG CYS 556 B CYS 578 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? 
disulf ? disulf9 C SG CYS 47 C CYS 69 1_555 C SG CYS 57 C CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? 
disulf ? disulf10 C SG CYS 63 C CYS 85 1_555 C SG CYS 206 C CYS 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf11 C SG CYS 414 C CYS 436 1_555 C SG CYS 415 C CYS 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? 
disulf ? disulf12 C SG CYS 468 C CYS 490 1_555 C SG CYS 556 C CYS 578 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf13 D SG CYS 47 D CYS 69 1_555 D SG CYS 57 D CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
disulf ? disulf14 D SG CYS 63 D CYS 85 1_555 D SG CYS 206 D CYS 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
disulf ? disulf15 D SG CYS 414 D CYS 436 1_555 D SG CYS 415 D CYS 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? 
disulf ? disulf16 D SG CYS 468 D CYS 490 1_555 D SG CYS 556 D CYS 578 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
covale ? covale1 A ND2 ASN 77 A ASN 99 1_555 F C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.472 ? 
covale ? covale2 A ND2 ASN 254 A ASN 276 1_555 G C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.485 ? 
covale ? covale3 B ND2 ASN 77 B ASN 99 1_555 K C1 NAG . B NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? 
covale ? covale4 C ND2 ASN 77 C ASN 99 1_555 O C1 NAG . C NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? 
covale ? covale5 C ND2 ASN 254 C ASN 276 1_555 P C1 NAG . C NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? 
covale ? covale6 D ND2 ASN 521 D ASN 543 1_555 T C1 NAG . D NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? 
#
_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 410 n n 
N1 C6 UDP sing 411 n n 
N1 C1' UDP sing 412 n n 
C2 N3 UDP sing 413 n n 
C2 O2 UDP doub 414 n n 
N3 C4 UDP sing 415 n n 
N3 HN3 UDP sing 416 n n 
C4 C5 UDP sing 417 n n 
C4 O4 UDP doub 418 n n 
C5 C6 UDP doub 419 n n 
C5 H5 UDP sing 420 n n 
C6 H6 UDP sing 421 n n 
C1' C2' UDP sing 422 n n 
C1' O4' UDP sing 423 n n 
C1' H1' UDP sing 424 n n 
C2' O2' UDP sing 425 n n 
C2' C3' UDP sing 426 n n 
C2' H2' UDP sing 427 n n 
O2' HO2' UDP sing 428 n n 
C3' C4' UDP sing 429 n n 
C3' O3' UDP sing 430 n n 
C3' H3' UDP sing 431 n n 
C4' O4' UDP sing 432 n n 
C4' C5' UDP sing 433 n n 
C4' H4' UDP sing 434 n n 
O3' HO3' UDP sing 435 n n 
C5' O5' UDP sing 436 n n 
C5' "H5'1" UDP sing 437 n n 
C5' "H5'2" UDP sing 438 n n 
O5' PA UDP sing 439 n n 
PA O1A UDP doub 440 n n 
PA O2A UDP sing 441 n n 
PA O3A UDP sing 442 n n 
O2A HOA2 UDP sing 443 n n 
O3A PB UDP sing 444 n n 
PB O1B UDP doub 445 n n 
PB O2B UDP sing 446 n n 
PB O3B UDP sing 447 n n 
O2B HOB2 UDP sing 448 n n 
O3B HOB3 UDP sing 449 n n 
#
_atom_sites.entry_id                     8KB7 
_atom_sites.fract_transf_matrix[1][1]    0.006896 
_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]    0.006667 
_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]    0.005222 
_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 UDP A 1 601 1000 UDP UDP . 
F 3 NAG A 1 602 1001 NAG NAG . 
G 3 NAG A 1 603 1003 NAG NAG . 
H 4 MAN A 1 604 2001 MAN MAN . 
I 5 CL A 1 605 2 CL CL . 
J 2 UDP B 1 601 1000 UDP UDP . 
K 3 NAG B 1 602 1001 NAG NAG . 
L 4 MAN B 1 603 2001 MAN MAN . 
M 5 CL B 1 604 1 CL CL . 
N 2 UDP C 1 601 1000 UDP UDP . 
O 3 NAG C 1 602 1001 NAG NAG . 
P 3 NAG C 1 603 1003 NAG NAG . 
Q 4 MAN C 1 604 2001 MAN MAN . 
R 5 CL C 1 605 3 CL CL . 
S 2 UDP D 1 601 1000 UDP UDP . 
T 3 NAG D 1 602 1004 NAG NAG . 
U 4 MAN D 1 603 2001 MAN MAN . 
V 5 CL D 1 604 4 CL CL . 
#
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 . . . E 2 100.225 60.958 -16.06 1 120.28 ? N1 UDP 601 A 1 
HETATM 2 C C2 UDP . . . E 2 100.795 62.147 -16.614 1 126.13 ? C2 UDP 601 A 1 
HETATM 3 N N3 UDP . . . E 2 101.679 62.061 -17.614 1 126.97 ? N3 UDP 601 A 1 
HETATM 4 C C4 UDP . . . E 2 102.056 60.88 -18.114 1 119.49 ? C4 UDP 601 A 1 
HETATM 5 C C5 UDP . . . E 2 101.529 59.705 -17.587 1 125.95 ? C5 UDP 601 A 1 
HETATM 6 C C6 UDP . . . E 2 100.598 59.769 -16.552 1 123.62 ? C6 UDP 601 A 1 
HETATM 7 O O2 UDP . . . E 2 100.491 63.301 -16.222 1 141.59 ? O2 UDP 601 A 1 
HETATM 8 O O4 UDP . . . E 2 102.889 60.845 -19.047 1 119.79 ? O4 UDP 601 A 1 
HETATM 9 C C1' UDP . . . E 2 99.222 61.027 -14.98 1 115.72 ? C1' UDP 601 A 1 
HETATM 10 C C2' UDP . . . E 2 97.797 61.136 -15.521 1 103.22 ? C2' UDP 601 A 1 
HETATM 11 O O2' UDP . . . E 2 97.511 62.456 -16.019 1 104.67 ? O2' UDP 601 A 1 
HETATM 12 C C3' UDP . . . E 2 96.965 60.712 -14.318 1 98.23 ? C3' UDP 601 A 1 
HETATM 13 C C4' UDP . . . E 2 97.848 59.634 -13.702 1 103.63 ? C4' UDP 601 A 1 
HETATM 14 O O4' UDP . . . E 2 99.183 59.869 -14.151 1 113.63 ? O4' UDP 601 A 1 
HETATM 15 O O3' UDP . . . E 2 96.752 61.768 -13.353 1 75.31 ? O3' UDP 601 A 1 
HETATM 16 C C5' UDP . . . E 2 97.454 58.228 -14.118 1 93.77 ? C5' UDP 601 A 1 
HETATM 17 O O5' UDP . . . E 2 97.561 58.17 -15.545 1 88.27 ? O5' UDP 601 A 1 
HETATM 18 P PA UDP . . . E 2 96.59 57.225 -16.443 1 86.64 ? PA UDP 601 A 1 
HETATM 19 O O1A UDP . . . E 2 97.283 56.731 -17.722 1 86.33 ? O1A UDP 601 A 1 
HETATM 20 O O2A UDP . . . E 2 95.911 56.123 -15.622 1 73.76 ? O2A UDP 601 A 1 
HETATM 21 O O3A UDP . . . E 2 95.56 58.469 -16.791 1 96.46 ? O3A UDP 601 A 1 
HETATM 22 P PB UDP . . . E 2 94.469 58.459 -18.011 1 86.77 ? PB UDP 601 A 1 
HETATM 23 O O1B UDP . . . E 2 95.218 59.066 -19.191 1 96.42 ? O1B UDP 601 A 1 
HETATM 24 O O2B UDP . . . E 2 93.329 59.312 -17.499 1 99.75 ? O2B UDP 601 A 1 
HETATM 25 O O3B UDP . . . E 2 94.066 56.98 -18.178 1 91.58 ? O3B UDP 601 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           250 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           25 
#