data_5CLL
#
_model_server_result.job_id            1jWkSL4yBE8SXptNbvnNEw 
_model_server_result.datetime_utc      '2025-07-03 08:52:30' 
_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          5cll 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":200}' 
#
_entry.id    5CLL 
#
_exptl.entry_id    5CLL 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-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          90.05 
_cell.angle_gamma         90 
_cell.entry_id            5CLL 
_cell.length_a            50.6 
_cell.length_b            55.78 
_cell.length_c            122.93 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5CLL 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? dimeric 2 author_defined_assembly 1 
? dimeric 2 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,B,E,F,G,K,L 1 1 
C,D,H,I,J,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
metalc ? metalc1 A OG1 THR 24 A THR 24 1_555 G MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.858 ? 
metalc ? metalc2 A OG1 THR 42 A THR 42 1_555 G MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
metalc ? metalc3 E O2B GDP . A GDP 200 1_555 F BE BEF . A BEF 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.759 ? 
metalc ? metalc4 E O3B GDP . A GDP 200 1_555 G MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
metalc ? metalc5 G MG MG . A MG 202 1_555 K O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? 
metalc ? metalc6 G MG MG . A MG 202 1_555 K O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? 
metalc ? metalc7 C OG1 THR 24 C THR 24 1_555 J MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.923 ? 
metalc ? metalc8 C OG1 THR 42 C THR 42 1_555 J MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? 
metalc ? metalc9 H O1B GDP . C GDP 200 1_555 J MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? 
metalc ? metalc10 J MG MG . C MG 202 1_555 M O HOH . C HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? 
metalc ? metalc11 J MG MG . C MG 202 1_555 M O HOH . C HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? 
#
_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 86 n n 
PB O2B GDP sing 87 n n 
PB O3B GDP sing 88 n n 
PB O3A GDP sing 89 n n 
O2B HOB2 GDP sing 90 n n 
O3B HOB3 GDP sing 91 n n 
O3A PA GDP sing 92 n n 
PA O1A GDP doub 93 n n 
PA O2A GDP sing 94 n n 
PA O5' GDP sing 95 n n 
O2A HOA2 GDP sing 96 n n 
O5' C5' GDP sing 97 n n 
C5' C4' GDP sing 98 n n 
C5' H5' GDP sing 99 n n 
C5' "H5''" GDP sing 100 n n 
C4' O4' GDP sing 101 n n 
C4' C3' GDP sing 102 n n 
C4' H4' GDP sing 103 n n 
O4' C1' GDP sing 104 n n 
C3' O3' GDP sing 105 n n 
C3' C2' GDP sing 106 n n 
C3' H3' GDP sing 107 n n 
O3' HO3' GDP sing 108 n n 
C2' O2' GDP sing 109 n n 
C2' C1' GDP sing 110 n n 
C2' H2' GDP sing 111 n n 
O2' HO2' GDP sing 112 n n 
C1' N9 GDP sing 113 n n 
C1' H1' GDP sing 114 n n 
N9 C8 GDP sing 115 n y 
N9 C4 GDP sing 116 n y 
C8 N7 GDP doub 117 n y 
C8 H8 GDP sing 118 n n 
N7 C5 GDP sing 119 n y 
C5 C6 GDP sing 120 n n 
C5 C4 GDP doub 121 n y 
C6 O6 GDP doub 122 n n 
C6 N1 GDP sing 123 n n 
N1 C2 GDP sing 124 n n 
N1 HN1 GDP sing 125 n n 
C2 N2 GDP sing 126 n n 
C2 N3 GDP doub 127 n n 
N2 HN21 GDP sing 128 n n 
N2 HN22 GDP sing 129 n n 
N3 C4 GDP sing 130 n n 
#
_atom_sites.entry_id                     5CLL 
_atom_sites.fract_transf_matrix[1][1]    0.019763 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000018 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.017928 
_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]    0.008135 
_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 GDP A 1 200 200 GDP GDP . 
F 4 BEF A 1 201 201 BEF BEF . 
G 5 MG A 1 202 202 MG MG . 
H 3 GDP C 1 200 200 GDP GDP . 
I 4 BEF C 1 201 201 BEF BEF . 
J 5 MG C 1 202 202 MG MG . 
K 6 HOH A 1 301 12 HOH HOH . 
K 6 HOH A 2 302 3 HOH HOH . 
K 6 HOH A 3 303 29 HOH HOH . 
K 6 HOH A 4 304 16 HOH HOH . 
K 6 HOH A 5 305 13 HOH HOH . 
K 6 HOH A 6 306 1 HOH HOH . 
K 6 HOH A 7 307 6 HOH HOH . 
K 6 HOH A 8 308 19 HOH HOH . 
K 6 HOH A 9 309 8 HOH HOH . 
K 6 HOH A 10 310 15 HOH HOH . 
L 6 HOH B 1 201 33 HOH HOH . 
L 6 HOH B 2 202 30 HOH HOH . 
L 6 HOH B 3 203 10 HOH HOH . 
L 6 HOH B 4 204 35 HOH HOH . 
L 6 HOH B 5 205 26 HOH HOH . 
L 6 HOH B 6 206 34 HOH HOH . 
M 6 HOH C 1 301 27 HOH HOH . 
M 6 HOH C 2 302 4 HOH HOH . 
M 6 HOH C 3 303 22 HOH HOH . 
M 6 HOH C 4 304 24 HOH HOH . 
M 6 HOH C 5 305 5 HOH HOH . 
M 6 HOH C 6 306 31 HOH HOH . 
M 6 HOH C 7 307 11 HOH HOH . 
M 6 HOH C 8 308 20 HOH HOH . 
M 6 HOH C 9 309 21 HOH HOH . 
M 6 HOH C 10 310 18 HOH HOH . 
M 6 HOH C 11 311 17 HOH HOH . 
M 6 HOH C 12 312 25 HOH HOH . 
N 6 HOH D 1 201 28 HOH HOH . 
N 6 HOH D 2 202 7 HOH HOH . 
N 6 HOH D 3 203 23 HOH HOH . 
N 6 HOH D 4 204 2 HOH HOH . 
N 6 HOH D 5 205 32 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 . . . E 3 20.834 -10.324 9.727 1 24.62 ? PB GDP 200 A 1 
HETATM 2 O O1B GDP . . . E 3 20.011 -10.519 8.477 1 24.69 ? O1B GDP 200 A 1 
HETATM 3 O O2B GDP . . . E 3 22.235 -10.887 9.681 1 24.38 ? O2B GDP 200 A 1 
HETATM 4 O O3B GDP . . . E 3 20.1 -10.586 11.02 1 23.99 ? O3B GDP 200 A 1 
HETATM 5 O O3A GDP . . . E 3 21.049 -8.722 9.676 1 25.52 ? O3A GDP 200 A 1 
HETATM 6 P PA GDP . . . E 3 20.564 -7.721 10.844 1 24.23 ? PA GDP 200 A 1 
HETATM 7 O O1A GDP . . . E 3 19.066 -7.64 10.833 1 24.95 ? O1A GDP 200 A 1 
HETATM 8 O O2A GDP . . . E 3 21.28 -8.111 12.104 1 24.6 ? O2A GDP 200 A 1 
HETATM 9 O O5' GDP . . . E 3 21.12 -6.313 10.316 1 25.26 ? O5' GDP 200 A 1 
HETATM 10 C C5' GDP . . . E 3 20.742 -5.852 9.021 1 24.77 ? C5' GDP 200 A 1 
HETATM 11 C C4' GDP . . . E 3 20.985 -4.347 8.891 1 24.68 ? C4' GDP 200 A 1 
HETATM 12 O O4' GDP . . . E 3 20.168 -3.841 7.827 1 23.94 ? O4' GDP 200 A 1 
HETATM 13 C C3' GDP . . . E 3 20.614 -3.551 10.142 1 24.19 ? C3' GDP 200 A 1 
HETATM 14 O O3' GDP . . . E 3 21.467 -2.412 10.226 1 24.55 ? O3' GDP 200 A 1 
HETATM 15 C C2' GDP . . . E 3 19.242 -3.022 9.839 1 24.33 ? C2' GDP 200 A 1 
HETATM 16 O O2' GDP . . . E 3 18.981 -1.763 10.463 1 25 ? O2' GDP 200 A 1 
HETATM 17 C C1' GDP . . . E 3 19.256 -2.87 8.33 1 23.97 ? C1' GDP 200 A 1 
HETATM 18 N N9 GDP . . . E 3 17.887 -3.131 7.87 1 23.84 ? N9 GDP 200 A 1 
HETATM 19 C C8 GDP . . . E 3 17.12 -4.189 8.185 1 23.76 ? C8 GDP 200 A 1 
HETATM 20 N N7 GDP . . . E 3 15.895 -4.09 7.61 1 23.81 ? N7 GDP 200 A 1 
HETATM 21 C C5 GDP . . . E 3 15.88 -2.944 6.904 1 24.65 ? C5 GDP 200 A 1 
HETATM 22 C C6 GDP . . . E 3 14.911 -2.208 6.062 1 24.55 ? C6 GDP 200 A 1 
HETATM 23 O O6 GDP . . . E 3 13.771 -2.646 5.835 1 24.24 ? O6 GDP 200 A 1 
HETATM 24 N N1 GDP . . . E 3 15.303 -1.046 5.535 1 25.64 ? N1 GDP 200 A 1 
HETATM 25 C C2 GDP . . . E 3 16.519 -0.513 5.742 1 24.99 ? C2 GDP 200 A 1 
HETATM 26 N N2 GDP . . . E 3 16.815 0.672 5.149 1 25.88 ? N2 GDP 200 A 1 
HETATM 27 N N3 GDP . . . E 3 17.449 -1.12 6.505 1 24.27 ? N3 GDP 200 A 1 
HETATM 28 C C4 GDP . . . E 3 17.194 -2.311 7.09 1 24.31 ? C4 GDP 200 A 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           34 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           339 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#