data_5GGI
#
_model_server_result.job_id            EiocPSqpLMDS1zFSq7oTZg 
_model_server_result.datetime_utc      '2024-12-03 02:43:34' 
_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          5ggi 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":701}' 
#
_entry.id    5GGI 
#
_exptl.entry_id    5GGI 
_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            5GGI 
_cell.length_a            68.162 
_cell.length_b            126.539 
_cell.length_c            172.865 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5GGI 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 2 21 21' 
#
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 
? trimeric 3 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,G,L 1 1 
B,C,D,H,I,J,K,M,N 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 E 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 163 A CYS 254 1_555 A SG CYS 190 A CYS 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? 
disulf ? disulf2 A SG CYS 178 A CYS 269 1_555 A SG CYS 188 A CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf3 A SG CYS 330 A CYS 421 1_555 A SG CYS 399 A CYS 490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf4 A SG CYS 471 A CYS 562 1_555 A SG CYS 505 A CYS 596 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf5 B SG CYS 163 B CYS 254 1_555 B SG CYS 190 B CYS 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 
disulf ? disulf6 B SG CYS 178 B CYS 269 1_555 B SG CYS 188 B CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
disulf ? disulf7 B SG CYS 330 B CYS 421 1_555 B SG CYS 399 B CYS 490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf8 B SG CYS 471 B CYS 562 1_555 B SG CYS 505 B CYS 596 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
covale ? covale1 C C ACE 1 F ACE 0 1_555 C N ALA 2 F ALA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
covale ? covale2 C OG1 THR 5 F THR 4 1_555 J C1 MAN . F MAN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? 
covale ? covale3 D OG1 THR 5 G THR 4 1_555 K C1 MAN . G MAN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
metalc ? metalc1 A OD2 ASP 304 A ASP 395 1_555 F MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
metalc ? metalc2 A NE2 HIS 409 A HIS 500 1_555 F MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? 
metalc ? metalc3 E O2A UDP . A UDP 701 1_555 F MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? 
metalc ? metalc4 B OD2 ASP 304 B ASP 395 1_555 I MN MN . B MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? 
metalc ? metalc5 B NE2 HIS 409 B HIS 500 1_555 I MN MN . B MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? 
metalc ? metalc6 H O2A UDP . B UDP 701 1_555 I MN MN . B MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? 
metalc ? metalc7 H O2B UDP . B UDP 701 1_555 I MN MN . B MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? 
#
_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 394 n n 
N1 C6 UDP sing 395 n n 
N1 C1' UDP sing 396 n n 
C2 N3 UDP sing 397 n n 
C2 O2 UDP doub 398 n n 
N3 C4 UDP sing 399 n n 
N3 HN3 UDP sing 400 n n 
C4 C5 UDP sing 401 n n 
C4 O4 UDP doub 402 n n 
C5 C6 UDP doub 403 n n 
C5 H5 UDP sing 404 n n 
C6 H6 UDP sing 405 n n 
C1' C2' UDP sing 406 n n 
C1' O4' UDP sing 407 n n 
C1' H1' UDP sing 408 n n 
C2' O2' UDP sing 409 n n 
C2' C3' UDP sing 410 n n 
C2' H2' UDP sing 411 n n 
O2' HO2' UDP sing 412 n n 
C3' C4' UDP sing 413 n n 
C3' O3' UDP sing 414 n n 
C3' H3' UDP sing 415 n n 
C4' O4' UDP sing 416 n n 
C4' C5' UDP sing 417 n n 
C4' H4' UDP sing 418 n n 
O3' HO3' UDP sing 419 n n 
C5' O5' UDP sing 420 n n 
C5' "H5'1" UDP sing 421 n n 
C5' "H5'2" UDP sing 422 n n 
O5' PA UDP sing 423 n n 
PA O1A UDP doub 424 n n 
PA O2A UDP sing 425 n n 
PA O3A UDP sing 426 n n 
O2A HOA2 UDP sing 427 n n 
O3A PB UDP sing 428 n n 
PB O1B UDP doub 429 n n 
PB O2B UDP sing 430 n n 
PB O3B UDP sing 431 n n 
O2B HOB2 UDP sing 432 n n 
O3B HOB3 UDP sing 433 n n 
#
_atom_sites.entry_id                     5GGI 
_atom_sites.fract_transf_matrix[1][1]    0.014671 
_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]    0.007903 
_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]    0.005785 
_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 1 701 1 UDP UDP . 
F 4 MN A 1 702 5 MN MN . 
G 5 PO4 A 1 703 1 PO4 PO4 . 
H 3 UDP B 1 701 2 UDP UDP . 
I 4 MN B 1 702 4 MN MN . 
J 6 MAN F 1 101 11 MAN MAN . 
K 6 MAN G 1 101 11 MAN MAN . 
L 7 HOH A 1 801 21 HOH HOH . 
L 7 HOH A 2 802 14 HOH HOH . 
L 7 HOH A 3 803 27 HOH HOH . 
L 7 HOH A 4 804 74 HOH HOH . 
L 7 HOH A 5 805 39 HOH HOH . 
L 7 HOH A 6 806 35 HOH HOH . 
L 7 HOH A 7 807 66 HOH HOH . 
L 7 HOH A 8 808 31 HOH HOH . 
L 7 HOH A 9 809 78 HOH HOH . 
L 7 HOH A 10 810 105 HOH HOH . 
L 7 HOH A 11 811 3 HOH HOH . 
L 7 HOH A 12 812 18 HOH HOH . 
L 7 HOH A 13 813 30 HOH HOH . 
L 7 HOH A 14 814 67 HOH HOH . 
L 7 HOH A 15 815 13 HOH HOH . 
L 7 HOH A 16 816 10 HOH HOH . 
L 7 HOH A 17 817 55 HOH HOH . 
L 7 HOH A 18 818 9 HOH HOH . 
L 7 HOH A 19 819 85 HOH HOH . 
L 7 HOH A 20 820 91 HOH HOH . 
L 7 HOH A 21 821 45 HOH HOH . 
L 7 HOH A 22 822 106 HOH HOH . 
L 7 HOH A 23 823 38 HOH HOH . 
L 7 HOH A 24 824 20 HOH HOH . 
L 7 HOH A 25 825 25 HOH HOH . 
L 7 HOH A 26 826 52 HOH HOH . 
L 7 HOH A 27 827 84 HOH HOH . 
L 7 HOH A 28 828 57 HOH HOH . 
L 7 HOH A 29 829 107 HOH HOH . 
L 7 HOH A 30 830 44 HOH HOH . 
L 7 HOH A 31 831 63 HOH HOH . 
L 7 HOH A 32 832 49 HOH HOH . 
L 7 HOH A 33 833 5 HOH HOH . 
L 7 HOH A 34 834 12 HOH HOH . 
L 7 HOH A 35 835 61 HOH HOH . 
L 7 HOH A 36 836 101 HOH HOH . 
L 7 HOH A 37 837 26 HOH HOH . 
L 7 HOH A 38 838 42 HOH HOH . 
L 7 HOH A 39 839 17 HOH HOH . 
L 7 HOH A 40 840 32 HOH HOH . 
L 7 HOH A 41 841 40 HOH HOH . 
L 7 HOH A 42 842 75 HOH HOH . 
L 7 HOH A 43 843 7 HOH HOH . 
L 7 HOH A 44 844 72 HOH HOH . 
L 7 HOH A 45 845 79 HOH HOH . 
L 7 HOH A 46 846 41 HOH HOH . 
L 7 HOH A 47 847 28 HOH HOH . 
L 7 HOH A 48 848 82 HOH HOH . 
L 7 HOH A 49 849 8 HOH HOH . 
L 7 HOH A 50 850 95 HOH HOH . 
L 7 HOH A 51 851 86 HOH HOH . 
M 7 HOH B 1 801 62 HOH HOH . 
M 7 HOH B 2 802 76 HOH HOH . 
M 7 HOH B 3 803 70 HOH HOH . 
M 7 HOH B 4 804 51 HOH HOH . 
M 7 HOH B 5 805 59 HOH HOH . 
M 7 HOH B 6 806 73 HOH HOH . 
M 7 HOH B 7 807 1 HOH HOH . 
M 7 HOH B 8 808 33 HOH HOH . 
M 7 HOH B 9 809 104 HOH HOH . 
M 7 HOH B 10 810 102 HOH HOH . 
M 7 HOH B 11 811 50 HOH HOH . 
M 7 HOH B 12 812 15 HOH HOH . 
M 7 HOH B 13 813 97 HOH HOH . 
M 7 HOH B 14 814 2 HOH HOH . 
M 7 HOH B 15 815 54 HOH HOH . 
M 7 HOH B 16 816 48 HOH HOH . 
M 7 HOH B 17 817 56 HOH HOH . 
M 7 HOH B 18 818 99 HOH HOH . 
M 7 HOH B 19 819 103 HOH HOH . 
M 7 HOH B 20 820 64 HOH HOH . 
M 7 HOH B 21 821 11 HOH HOH . 
M 7 HOH B 22 822 87 HOH HOH . 
M 7 HOH B 23 823 94 HOH HOH . 
M 7 HOH B 24 824 53 HOH HOH . 
M 7 HOH B 25 825 37 HOH HOH . 
M 7 HOH B 26 826 100 HOH HOH . 
M 7 HOH B 27 827 4 HOH HOH . 
M 7 HOH B 28 828 83 HOH HOH . 
M 7 HOH B 29 829 58 HOH HOH . 
M 7 HOH B 30 830 43 HOH HOH . 
M 7 HOH B 31 831 98 HOH HOH . 
M 7 HOH B 32 832 34 HOH HOH . 
M 7 HOH B 33 833 65 HOH HOH . 
M 7 HOH B 34 834 36 HOH HOH . 
M 7 HOH B 35 835 60 HOH HOH . 
M 7 HOH B 36 836 16 HOH HOH . 
M 7 HOH B 37 837 24 HOH HOH . 
M 7 HOH B 38 838 6 HOH HOH . 
M 7 HOH B 39 839 47 HOH HOH . 
M 7 HOH B 40 840 69 HOH HOH . 
M 7 HOH B 41 841 29 HOH HOH . 
M 7 HOH B 42 842 23 HOH HOH . 
M 7 HOH B 43 843 46 HOH HOH . 
M 7 HOH B 44 844 71 HOH HOH . 
M 7 HOH B 45 845 96 HOH HOH . 
M 7 HOH B 46 846 89 HOH HOH . 
M 7 HOH B 47 847 92 HOH HOH . 
M 7 HOH B 48 848 68 HOH HOH . 
N 7 HOH G 1 201 108 HOH HOH . 
N 7 HOH G 2 202 77 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 . . . E 3 22.261 163.471 16.87 1 102.82 ? N1 UDP 701 A 1 
HETATM 2 C C2 UDP . . . E 3 22.378 164.23 15.721 1 96.91 ? C2 UDP 701 A 1 
HETATM 3 N N3 UDP . . . E 3 23.016 165.455 15.754 1 94.22 ? N3 UDP 701 A 1 
HETATM 4 C C4 UDP . . . E 3 23.54 165.925 16.942 1 92.63 ? C4 UDP 701 A 1 
HETATM 5 C C5 UDP . . . E 3 23.418 165.158 18.097 1 97.48 ? C5 UDP 701 A 1 
HETATM 6 C C6 UDP . . . E 3 22.67 163.985 18.069 1 100.33 ? C6 UDP 701 A 1 
HETATM 7 O O2 UDP . . . E 3 21.908 163.81 14.665 1 95.73 ? O2 UDP 701 A 1 
HETATM 8 O O4 UDP . . . E 3 24.111 167.016 16.977 1 84.14 ? O4 UDP 701 A 1 
HETATM 9 C C1' UDP . . . E 3 21.566 162.168 16.805 1 108.86 ? C1' UDP 701 A 1 
HETATM 10 C C2' UDP . . . E 3 22.514 161.013 17.087 1 110.66 ? C2' UDP 701 A 1 
HETATM 11 O O2' UDP . . . E 3 22.955 160.407 15.899 1 108.3 ? O2' UDP 701 A 1 
HETATM 12 C C3' UDP . . . E 3 21.688 160.041 17.908 1 114.61 ? C3' UDP 701 A 1 
HETATM 13 C C4' UDP . . . E 3 20.497 160.845 18.412 1 116.93 ? C4' UDP 701 A 1 
HETATM 14 O O4' UDP . . . E 3 20.526 162.102 17.765 1 112.24 ? O4' UDP 701 A 1 
HETATM 15 O O3' UDP . . . E 3 21.258 158.97 17.101 1 114.96 ? O3' UDP 701 A 1 
HETATM 16 C C5' UDP . . . E 3 20.595 161.057 19.917 1 124.44 ? C5' UDP 701 A 1 
HETATM 17 O O5' UDP . . . E 3 21.961 160.917 20.231 1 134.26 ? O5' UDP 701 A 1 
HETATM 18 P PA UDP . . . E 3 22.608 161.071 21.696 1 145.26 ? PA UDP 701 A 1 
HETATM 19 O O1A UDP . . . E 3 23.781 161.971 21.647 1 143.52 ? O1A UDP 701 A 1 
HETATM 20 O O2A UDP . . . E 3 22.999 159.718 22.152 1 155.11 ? O2A UDP 701 A 1 
HETATM 21 O O3A UDP . . . E 3 21.477 161.652 22.688 1 148.86 ? O3A UDP 701 A 1 
HETATM 22 P PB UDP . . . E 3 21.332 161.083 24.191 1 144.1 ? PB UDP 701 A 1 
HETATM 23 O O1B UDP . . . E 3 20.607 159.792 24.151 1 144.06 ? O1B UDP 701 A 1 
HETATM 24 O O2B UDP . . . E 3 22.679 160.86 24.763 1 142.81 ? O2B UDP 701 A 1 
HETATM 25 O O3B UDP . . . E 3 20.6 162.056 25.032 1 144 ? O3B UDP 701 A 1 
#
_model_server_stats.io_time_ms              88 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           269 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           25 
#