data_6UT5
#
_model_server_result.job_id            XJXWNsZVvJtDHBFXwlbVdg 
_model_server_result.datetime_utc      '2024-10-19 16:27:45' 
_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          6ut5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"R","auth_seq_id":701}' 
#
_entry.id    6UT5 
#
_exptl.entry_id    6UT5 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_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            6UT5 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6UT5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    heptameric 
_pdbx_struct_assembly.oligomeric_count      7 
_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,M,N,O,P,Q,R,S,T,U,V,W,X,Y 
_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    ? 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      5 
_struct_asym.id                             R 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 OG1 THR 222 A THR 222 1_555 I MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? 
metalc ? metalc2 A OD1 ASP 356 A ASP 356 1_555 I MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.865 ? 
metalc ? metalc3 H O3G GSP . A GSP 701 1_555 I MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? 
metalc ? metalc4 H O2B GSP . A GSP 701 1_555 I MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.713 ? 
metalc ? metalc5 I MG MG . A MG 702 1_555 T O HOH . A HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? 
metalc ? metalc6 I MG MG . A MG 702 1_555 T O HOH . A HOH 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? 
metalc ? metalc7 B OG1 THR 222 B THR 222 1_555 K MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? 
metalc ? metalc8 B OD1 ASP 356 B ASP 356 1_555 K MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? 
metalc ? metalc9 J O2G GSP . B GSP 701 1_555 K MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? 
metalc ? metalc10 J O1B GSP . B GSP 701 1_555 K MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.77 ? 
metalc ? metalc11 K MG MG . B MG 702 1_555 U O HOH . B HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? 
metalc ? metalc12 K MG MG . B MG 702 1_555 U O HOH . B HOH 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? 
metalc ? metalc13 C OG1 THR 222 C THR 222 1_555 M MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? 
metalc ? metalc14 C OD2 ASP 356 C ASP 356 1_555 M MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.927 ? 
metalc ? metalc15 L O2G GSP . C GSP 701 1_555 M MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? 
metalc ? metalc16 L O2B GSP . C GSP 701 1_555 M MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.947 ? 
metalc ? metalc17 M MG MG . C MG 702 1_555 V O HOH . C HOH 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? 
metalc ? metalc18 M MG MG . C MG 702 1_555 V O HOH . C HOH 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? 
metalc ? metalc19 D OG1 THR 222 D THR 222 1_555 O MG MG . D MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? 
metalc ? metalc20 N O2G GSP . D GSP 701 1_555 O MG MG . D MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
metalc ? metalc21 N O1B GSP . D GSP 701 1_555 O MG MG . D MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc22 O MG MG . D MG 702 1_555 W O HOH . D HOH 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? 
metalc ? metalc23 O MG MG . D MG 702 1_555 W O HOH . D HOH 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.67 ? 
metalc ? metalc24 O MG MG . D MG 702 1_555 W O HOH . D HOH 807 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? 
metalc ? metalc25 E OG1 THR 222 E THR 222 1_555 Q MG MG . E MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
metalc ? metalc26 P O3G GSP . E GSP 701 1_555 Q MG MG . E MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? 
metalc ? metalc27 P O1B GSP . E GSP 701 1_555 Q MG MG . E MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? 
metalc ? metalc28 Q MG MG . E MG 702 1_555 X O HOH . E HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? 
metalc ? metalc29 Q MG MG . E MG 702 1_555 X O HOH . E HOH 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? 
metalc ? metalc30 Q MG MG . E MG 702 1_555 X O HOH . E HOH 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? 
metalc ? metalc31 F OG1 THR 222 F THR 222 1_555 S MG MG . F MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? 
metalc ? metalc32 R O1B GDP . F GDP 701 1_555 S MG MG . F MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? 
metalc ? metalc33 S MG MG . F MG 702 1_555 Y O HOH . F HOH 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? 
metalc ? metalc34 S MG MG . F MG 702 1_555 Y O HOH . F HOH 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? 
#
_chem_comp.formula           'C10 H15 N5 O11 P2' 
_chem_comp.formula_weight    443.201 
_chem_comp.id                GDP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "GUANOSINE-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
PB O1B GDP doub 83 n n 
PB O2B GDP sing 84 n n 
PB O3B GDP sing 85 n n 
PB O3A GDP sing 86 n n 
O2B HOB2 GDP sing 87 n n 
O3B HOB3 GDP sing 88 n n 
O3A PA GDP sing 89 n n 
PA O1A GDP doub 90 n n 
PA O2A GDP sing 91 n n 
PA O5' GDP sing 92 n n 
O2A HOA2 GDP sing 93 n n 
O5' C5' GDP sing 94 n n 
C5' C4' GDP sing 95 n n 
C5' H5' GDP sing 96 n n 
C5' "H5''" GDP sing 97 n n 
C4' O4' GDP sing 98 n n 
C4' C3' GDP sing 99 n n 
C4' H4' GDP sing 100 n n 
O4' C1' GDP sing 101 n n 
C3' O3' GDP sing 102 n n 
C3' C2' GDP sing 103 n n 
C3' H3' GDP sing 104 n n 
O3' HO3' GDP sing 105 n n 
C2' O2' GDP sing 106 n n 
C2' C1' GDP sing 107 n n 
C2' H2' GDP sing 108 n n 
O2' HO2' GDP sing 109 n n 
C1' N9 GDP sing 110 n n 
C1' H1' GDP sing 111 n n 
N9 C8 GDP sing 112 n y 
N9 C4 GDP sing 113 n y 
C8 N7 GDP doub 114 n y 
C8 H8 GDP sing 115 n n 
N7 C5 GDP sing 116 n y 
C5 C6 GDP sing 117 n n 
C5 C4 GDP doub 118 n y 
C6 O6 GDP doub 119 n n 
C6 N1 GDP sing 120 n n 
N1 C2 GDP sing 121 n n 
N1 HN1 GDP sing 122 n n 
C2 N2 GDP sing 123 n n 
C2 N3 GDP doub 124 n n 
N2 HN21 GDP sing 125 n n 
N2 HN22 GDP sing 126 n n 
N3 C4 GDP sing 127 n n 
#
_atom_sites.entry_id                     6UT5 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
H 3 GSP A 1 701 701 GSP GSP . 
I 4 MG A 1 702 801 MG MG . 
J 3 GSP B 1 701 701 GSP GSP . 
K 4 MG B 1 702 801 MG MG . 
L 3 GSP C 1 701 701 GSP GSP . 
M 4 MG C 1 702 801 MG MG . 
N 3 GSP D 1 701 701 GSP GSP . 
O 4 MG D 1 702 801 MG MG . 
P 3 GSP E 1 701 701 GSP GSP . 
Q 4 MG E 1 702 801 MG MG . 
R 5 GDP F 1 701 701 GDP GDP . 
S 4 MG F 1 702 801 MG MG . 
T 6 HOH A 1 801 902 HOH HOH . 
T 6 HOH A 2 802 901 HOH HOH . 
T 6 HOH A 3 803 903 HOH HOH . 
U 6 HOH B 1 801 902 HOH HOH . 
U 6 HOH B 2 802 904 HOH HOH . 
U 6 HOH B 3 803 903 HOH HOH . 
U 6 HOH B 4 804 901 HOH HOH . 
V 6 HOH C 1 901 901 HOH HOH . 
V 6 HOH C 2 902 903 HOH HOH . 
V 6 HOH C 3 903 905 HOH HOH . 
V 6 HOH C 4 904 904 HOH HOH . 
V 6 HOH C 5 905 902 HOH HOH . 
W 6 HOH D 1 801 904 HOH HOH . 
W 6 HOH D 2 802 907 HOH HOH . 
W 6 HOH D 3 803 905 HOH HOH . 
W 6 HOH D 4 804 903 HOH HOH . 
W 6 HOH D 5 805 901 HOH HOH . 
W 6 HOH D 6 806 906 HOH HOH . 
W 6 HOH D 7 807 902 HOH HOH . 
X 6 HOH E 1 801 903 HOH HOH . 
X 6 HOH E 2 802 904 HOH HOH . 
X 6 HOH E 3 803 901 HOH HOH . 
X 6 HOH E 4 804 902 HOH HOH . 
X 6 HOH E 5 805 906 HOH HOH . 
X 6 HOH E 6 806 905 HOH HOH . 
Y 6 HOH F 1 801 903 HOH HOH . 
Y 6 HOH F 2 802 901 HOH HOH . 
Y 6 HOH F 3 803 902 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 P PB GDP . . . R 5 229 208.783 186.713 1 43.09 ? PB GDP 701 F 1 
HETATM 2 O O1B GDP . . . R 5 228.076 208.178 185.691 1 43.09 ? O1B GDP 701 F 1 
HETATM 3 O O2B GDP . . . R 5 228.243 209.067 187.983 1 43.09 ? O2B GDP 701 F 1 
HETATM 4 O O3B GDP . . . R 5 230.117 207.82 186.997 1 43.09 ? O3B GDP 701 F 1 
HETATM 5 O O3A GDP . . . R 5 229.625 210.151 186.164 1 43.09 ? O3A GDP 701 F 1 
HETATM 6 P PA GDP . . . R 5 229.614 210.536 184.606 1 43.09 ? PA GDP 701 F 1 
HETATM 7 O O1A GDP . . . R 5 230.088 209.395 183.75 1 43.09 ? O1A GDP 701 F 1 
HETATM 8 O O2A GDP . . . R 5 228.245 210.986 184.168 1 43.09 ? O2A GDP 701 F 1 
HETATM 9 O O5' GDP . . . R 5 230.659 211.753 184.555 1 43.09 ? O5' GDP 701 F 1 
HETATM 10 C C5' GDP . . . R 5 230.218 213.064 184.218 1 43.09 ? C5' GDP 701 F 1 
HETATM 11 C C4' GDP . . . R 5 231.187 213.661 183.214 1 43.09 ? C4' GDP 701 F 1 
HETATM 12 O O4' GDP . . . R 5 232.527 213.425 183.644 1 43.09 ? O4' GDP 701 F 1 
HETATM 13 C C3' GDP . . . R 5 231.03 212.989 181.862 1 43.09 ? C3' GDP 701 F 1 
HETATM 14 O O3' GDP . . . R 5 230.549 213.923 180.895 1 43.09 ? O3' GDP 701 F 1 
HETATM 15 C C2' GDP . . . R 5 232.413 212.521 181.47 1 43.09 ? C2' GDP 701 F 1 
HETATM 16 O O2' GDP . . . R 5 232.745 213.024 180.175 1 43.09 ? O2' GDP 701 F 1 
HETATM 17 C C1' GDP . . . R 5 233.342 213.096 182.521 1 43.09 ? C1' GDP 701 F 1 
HETATM 18 N N9 GDP . . . R 5 234.377 212.112 182.907 1 43.09 ? N9 GDP 701 F 1 
HETATM 19 C C8 GDP . . . R 5 234.353 211.327 183.997 1 43.09 ? C8 GDP 701 F 1 
HETATM 20 N N7 GDP . . . R 5 235.456 210.542 184.059 1 43.09 ? N7 GDP 701 F 1 
HETATM 21 C C5 GDP . . . R 5 236.211 210.829 182.985 1 43.09 ? C5 GDP 701 F 1 
HETATM 22 C C6 GDP . . . R 5 237.504 210.364 182.439 1 43.09 ? C6 GDP 701 F 1 
HETATM 23 O O6 GDP . . . R 5 238.167 209.485 183.028 1 43.09 ? O6 GDP 701 F 1 
HETATM 24 N N1 GDP . . . R 5 237.938 210.913 181.299 1 43.09 ? N1 GDP 701 F 1 
HETATM 25 C C2 GDP . . . R 5 237.24 211.861 180.648 1 43.09 ? C2 GDP 701 F 1 
HETATM 26 N N2 GDP . . . R 5 237.75 212.364 179.5 1 43.09 ? N2 GDP 701 F 1 
HETATM 27 N N3 GDP . . . R 5 236.048 212.335 181.09 1 43.09 ? N3 GDP 701 F 1 
HETATM 28 C C4 GDP . . . R 5 235.494 211.862 182.229 1 43.09 ? C4 GDP 701 F 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    35 
_model_server_stats.query_time_ms           316 
_model_server_stats.encode_time_ms          13 
_model_server_stats.element_count           28 
#