data_5TB5
#
_model_server_result.job_id            t771gEqW6WrHLKddBBqo8Q 
_model_server_result.datetime_utc      '2024-11-19 10:27:04' 
_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          5tb5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":202}' 
#
_entry.id    5TB5 
#
_exptl.entry_id    5TB5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          4 
_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          92.4 
_cell.angle_gamma         90 
_cell.entry_id            5TB5 
_cell.length_a            58.386 
_cell.length_b            70.651 
_cell.length_c            94.307 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5TB5 
_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
? 4 F N N 
? 4 I 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
covale ? covale1 A C LYS 184 A LYS 184 1_555 A N CMT 185 A CMT 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale2 A SG CMT 185 A CMT 185 1_555 E C1 FAR . A FAR 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.769 ? 
covale ? covale3 C C LYS 184 C LYS 184 1_555 C N CMT 185 C CMT 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale4 C SG CMT 185 C CMT 185 1_555 H C1 FAR . C FAR 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? 
#
_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 148 n n 
PB O2B GDP sing 149 n n 
PB O3B GDP sing 150 n n 
PB O3A GDP sing 151 n n 
O2B HOB2 GDP sing 152 n n 
O3B HOB3 GDP sing 153 n n 
O3A PA GDP sing 154 n n 
PA O1A GDP doub 155 n n 
PA O2A GDP sing 156 n n 
PA O5' GDP sing 157 n n 
O2A HOA2 GDP sing 158 n n 
O5' C5' GDP sing 159 n n 
C5' C4' GDP sing 160 n n 
C5' H5' GDP sing 161 n n 
C5' "H5''" GDP sing 162 n n 
C4' O4' GDP sing 163 n n 
C4' C3' GDP sing 164 n n 
C4' H4' GDP sing 165 n n 
O4' C1' GDP sing 166 n n 
C3' O3' GDP sing 167 n n 
C3' C2' GDP sing 168 n n 
C3' H3' GDP sing 169 n n 
O3' HO3' GDP sing 170 n n 
C2' O2' GDP sing 171 n n 
C2' C1' GDP sing 172 n n 
C2' H2' GDP sing 173 n n 
O2' HO2' GDP sing 174 n n 
C1' N9 GDP sing 175 n n 
C1' H1' GDP sing 176 n n 
N9 C8 GDP sing 177 n y 
N9 C4 GDP sing 178 n y 
C8 N7 GDP doub 179 n y 
C8 H8 GDP sing 180 n n 
N7 C5 GDP sing 181 n y 
C5 C6 GDP sing 182 n n 
C5 C4 GDP doub 183 n y 
C6 O6 GDP doub 184 n n 
C6 N1 GDP sing 185 n n 
N1 C2 GDP sing 186 n n 
N1 HN1 GDP sing 187 n n 
C2 N2 GDP sing 188 n n 
C2 N3 GDP doub 189 n n 
N2 HN21 GDP sing 190 n n 
N2 HN22 GDP sing 191 n n 
N3 C4 GDP sing 192 n n 
#
_atom_sites.entry_id                     5TB5 
_atom_sites.fract_transf_matrix[1][1]    0.017127 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000717 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014154 
_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]    0.010613 
_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 FAR A 1 201 186 FAR FAR . 
F 4 GDP A 1 202 200 GDP GDP . 
G 5 EDO B 1 201 1 EDO EDO . 
H 3 FAR C 1 201 186 FAR FAR . 
I 4 GDP C 1 202 200 GDP GDP . 
J 5 EDO D 1 201 2 EDO EDO . 
K 6 HOH A 1 301 62 HOH HOH . 
K 6 HOH A 2 302 4 HOH HOH . 
K 6 HOH A 3 303 83 HOH HOH . 
K 6 HOH A 4 304 75 HOH HOH . 
K 6 HOH A 5 305 89 HOH HOH . 
K 6 HOH A 6 306 98 HOH HOH . 
K 6 HOH A 7 307 5 HOH HOH . 
K 6 HOH A 8 308 53 HOH HOH . 
K 6 HOH A 9 309 103 HOH HOH . 
K 6 HOH A 10 310 16 HOH HOH . 
K 6 HOH A 11 311 140 HOH HOH . 
K 6 HOH A 12 312 18 HOH HOH . 
K 6 HOH A 13 313 1 HOH HOH . 
K 6 HOH A 14 314 39 HOH HOH . 
K 6 HOH A 15 315 29 HOH HOH . 
K 6 HOH A 16 316 20 HOH HOH . 
K 6 HOH A 17 317 36 HOH HOH . 
K 6 HOH A 18 318 156 HOH HOH . 
K 6 HOH A 19 319 71 HOH HOH . 
K 6 HOH A 20 320 35 HOH HOH . 
K 6 HOH A 21 321 159 HOH HOH . 
K 6 HOH A 22 322 114 HOH HOH . 
K 6 HOH A 23 323 152 HOH HOH . 
K 6 HOH A 24 324 8 HOH HOH . 
K 6 HOH A 25 325 13 HOH HOH . 
K 6 HOH A 26 326 133 HOH HOH . 
K 6 HOH A 27 327 56 HOH HOH . 
K 6 HOH A 28 328 2 HOH HOH . 
K 6 HOH A 29 329 129 HOH HOH . 
K 6 HOH A 30 330 160 HOH HOH . 
K 6 HOH A 31 331 118 HOH HOH . 
K 6 HOH A 32 332 25 HOH HOH . 
K 6 HOH A 33 333 15 HOH HOH . 
K 6 HOH A 34 334 76 HOH HOH . 
K 6 HOH A 35 335 47 HOH HOH . 
K 6 HOH A 36 336 111 HOH HOH . 
K 6 HOH A 37 337 67 HOH HOH . 
K 6 HOH A 38 338 132 HOH HOH . 
K 6 HOH A 39 339 37 HOH HOH . 
K 6 HOH A 40 340 102 HOH HOH . 
K 6 HOH A 41 341 153 HOH HOH . 
K 6 HOH A 42 342 42 HOH HOH . 
K 6 HOH A 43 343 136 HOH HOH . 
K 6 HOH A 44 344 23 HOH HOH . 
K 6 HOH A 45 345 121 HOH HOH . 
K 6 HOH A 46 346 108 HOH HOH . 
K 6 HOH A 47 347 6 HOH HOH . 
K 6 HOH A 48 348 141 HOH HOH . 
K 6 HOH A 49 349 81 HOH HOH . 
K 6 HOH A 50 350 142 HOH HOH . 
K 6 HOH A 51 351 12 HOH HOH . 
K 6 HOH A 52 352 17 HOH HOH . 
K 6 HOH A 53 353 105 HOH HOH . 
K 6 HOH A 54 354 38 HOH HOH . 
K 6 HOH A 55 355 30 HOH HOH . 
K 6 HOH A 56 356 122 HOH HOH . 
K 6 HOH A 57 357 106 HOH HOH . 
K 6 HOH A 58 358 148 HOH HOH . 
K 6 HOH A 59 359 124 HOH HOH . 
K 6 HOH A 60 360 146 HOH HOH . 
K 6 HOH A 61 361 49 HOH HOH . 
K 6 HOH A 62 362 80 HOH HOH . 
K 6 HOH A 63 363 154 HOH HOH . 
K 6 HOH A 64 364 57 HOH HOH . 
K 6 HOH A 65 365 82 HOH HOH . 
K 6 HOH A 66 366 117 HOH HOH . 
K 6 HOH A 67 367 95 HOH HOH . 
K 6 HOH A 68 368 110 HOH HOH . 
L 6 HOH B 1 301 48 HOH HOH . 
L 6 HOH B 2 302 10 HOH HOH . 
L 6 HOH B 3 303 52 HOH HOH . 
L 6 HOH B 4 304 85 HOH HOH . 
L 6 HOH B 5 305 9 HOH HOH . 
L 6 HOH B 6 306 149 HOH HOH . 
L 6 HOH B 7 307 22 HOH HOH . 
L 6 HOH B 8 308 155 HOH HOH . 
L 6 HOH B 9 309 109 HOH HOH . 
L 6 HOH B 10 310 51 HOH HOH . 
L 6 HOH B 11 311 119 HOH HOH . 
L 6 HOH B 12 312 126 HOH HOH . 
L 6 HOH B 13 313 60 HOH HOH . 
L 6 HOH B 14 314 74 HOH HOH . 
L 6 HOH B 15 315 55 HOH HOH . 
L 6 HOH B 16 316 3 HOH HOH . 
L 6 HOH B 17 317 19 HOH HOH . 
L 6 HOH B 18 318 72 HOH HOH . 
L 6 HOH B 19 319 79 HOH HOH . 
L 6 HOH B 20 320 64 HOH HOH . 
L 6 HOH B 21 321 31 HOH HOH . 
L 6 HOH B 22 322 7 HOH HOH . 
L 6 HOH B 23 323 93 HOH HOH . 
L 6 HOH B 24 324 33 HOH HOH . 
L 6 HOH B 25 325 68 HOH HOH . 
L 6 HOH B 26 326 86 HOH HOH . 
L 6 HOH B 27 327 65 HOH HOH . 
L 6 HOH B 28 328 73 HOH HOH . 
L 6 HOH B 29 329 145 HOH HOH . 
L 6 HOH B 30 330 41 HOH HOH . 
L 6 HOH B 31 331 120 HOH HOH . 
L 6 HOH B 32 332 125 HOH HOH . 
L 6 HOH B 33 333 116 HOH HOH . 
L 6 HOH B 34 334 14 HOH HOH . 
L 6 HOH B 35 335 123 HOH HOH . 
L 6 HOH B 36 336 24 HOH HOH . 
L 6 HOH B 37 337 32 HOH HOH . 
L 6 HOH B 38 338 113 HOH HOH . 
L 6 HOH B 39 339 61 HOH HOH . 
L 6 HOH B 40 340 139 HOH HOH . 
L 6 HOH B 41 341 87 HOH HOH . 
L 6 HOH B 42 342 97 HOH HOH . 
L 6 HOH B 43 343 138 HOH HOH . 
L 6 HOH B 44 344 70 HOH HOH . 
L 6 HOH B 45 345 151 HOH HOH . 
L 6 HOH B 46 346 134 HOH HOH . 
L 6 HOH B 47 347 101 HOH HOH . 
L 6 HOH B 48 348 157 HOH HOH . 
L 6 HOH B 49 349 137 HOH HOH . 
M 6 HOH C 1 301 28 HOH HOH . 
M 6 HOH C 2 302 46 HOH HOH . 
M 6 HOH C 3 303 112 HOH HOH . 
M 6 HOH C 4 304 127 HOH HOH . 
M 6 HOH C 5 305 90 HOH HOH . 
M 6 HOH C 6 306 115 HOH HOH . 
M 6 HOH C 7 307 34 HOH HOH . 
M 6 HOH C 8 308 44 HOH HOH . 
M 6 HOH C 9 309 58 HOH HOH . 
M 6 HOH C 10 310 158 HOH HOH . 
M 6 HOH C 11 311 54 HOH HOH . 
M 6 HOH C 12 312 94 HOH HOH . 
M 6 HOH C 13 313 77 HOH HOH . 
M 6 HOH C 14 314 128 HOH HOH . 
M 6 HOH C 15 315 91 HOH HOH . 
M 6 HOH C 16 316 69 HOH HOH . 
M 6 HOH C 17 317 26 HOH HOH . 
M 6 HOH C 18 318 131 HOH HOH . 
M 6 HOH C 19 319 150 HOH HOH . 
M 6 HOH C 20 320 100 HOH HOH . 
N 6 HOH D 1 301 27 HOH HOH . 
N 6 HOH D 2 302 59 HOH HOH . 
N 6 HOH D 3 303 144 HOH HOH . 
N 6 HOH D 4 304 78 HOH HOH . 
N 6 HOH D 5 305 88 HOH HOH . 
N 6 HOH D 6 306 11 HOH HOH . 
N 6 HOH D 7 307 63 HOH HOH . 
N 6 HOH D 8 308 107 HOH HOH . 
N 6 HOH D 9 309 40 HOH HOH . 
N 6 HOH D 10 310 135 HOH HOH . 
N 6 HOH D 11 311 84 HOH HOH . 
N 6 HOH D 12 312 99 HOH HOH . 
N 6 HOH D 13 313 45 HOH HOH . 
N 6 HOH D 14 314 104 HOH HOH . 
N 6 HOH D 15 315 147 HOH HOH . 
N 6 HOH D 16 316 50 HOH HOH . 
N 6 HOH D 17 317 92 HOH HOH . 
N 6 HOH D 18 318 66 HOH HOH . 
N 6 HOH D 19 319 43 HOH HOH . 
N 6 HOH D 20 320 21 HOH HOH . 
N 6 HOH D 21 321 130 HOH HOH . 
N 6 HOH D 22 322 143 HOH HOH . 
N 6 HOH D 23 323 96 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 . . . F 4 24.136 -29.717 36.89 1 29 ? PB GDP 202 A 1 
HETATM 2 O O1B GDP . . . F 4 23.617 -29.545 35.501 1 28.83 ? O1B GDP 202 A 1 
HETATM 3 O O2B GDP . . . F 4 25.517 -29.169 37.084 1 27.84 ? O2B GDP 202 A 1 
HETATM 4 O O3B GDP . . . F 4 23.173 -29.374 37.978 1 27.69 ? O3B GDP 202 A 1 
HETATM 5 O O3A GDP . . . F 4 24.352 -31.3 37.01 1 28.27 ? O3A GDP 202 A 1 
HETATM 6 P PA GDP . . . F 4 23.266 -32.303 37.627 1 33.04 ? PA GDP 202 A 1 
HETATM 7 O O1A GDP . . . F 4 21.993 -32.153 36.859 1 30.2 ? O1A GDP 202 A 1 
HETATM 8 O O2A GDP . . . F 4 23.253 -32.179 39.117 1 30.61 ? O2A GDP 202 A 1 
HETATM 9 O O5' GDP . . . F 4 23.901 -33.725 37.242 1 35.18 ? O5' GDP 202 A 1 
HETATM 10 C C5' GDP . . . F 4 24.132 -34.077 35.883 1 31.76 ? C5' GDP 202 A 1 
HETATM 11 C C4' GDP . . . F 4 24.114 -35.591 35.734 1 29.21 ? C4' GDP 202 A 1 
HETATM 12 O O4' GDP . . . F 4 25.277 -36.156 36.335 1 30.98 ? O4' GDP 202 A 1 
HETATM 13 C C3' GDP . . . F 4 22.918 -36.199 36.438 1 39.31 ? C3' GDP 202 A 1 
HETATM 14 O O3' GDP . . . F 4 22.436 -37.273 35.634 1 41.62 ? O3' GDP 202 A 1 
HETATM 15 C C2' GDP . . . F 4 23.482 -36.711 37.744 1 40.12 ? C2' GDP 202 A 1 
HETATM 16 O O2' GDP . . . F 4 22.781 -37.851 38.243 1 37.72 ? O2' GDP 202 A 1 
HETATM 17 C C1' GDP . . . F 4 24.912 -37.052 37.379 1 31.07 ? C1' GDP 202 A 1 
HETATM 18 N N9 GDP . . . F 4 25.808 -36.872 38.536 1 37.75 ? N9 GDP 202 A 1 
HETATM 19 C C8 GDP . . . F 4 25.875 -35.789 39.321 1 35.59 ? C8 GDP 202 A 1 
HETATM 20 N N7 GDP . . . F 4 26.805 -35.951 40.288 1 36.22 ? N7 GDP 202 A 1 
HETATM 21 C C5 GDP . . . F 4 27.349 -37.164 40.125 1 28.4 ? C5 GDP 202 A 1 
HETATM 22 C C6 GDP . . . F 4 28.39 -37.961 40.804 1 32.25 ? C6 GDP 202 A 1 
HETATM 23 O O6 GDP . . . F 4 28.988 -37.506 41.795 1 33.01 ? O6 GDP 202 A 1 
HETATM 24 N N1 GDP . . . F 4 28.659 -39.176 40.322 1 32.87 ? N1 GDP 202 A 1 
HETATM 25 C C2 GDP . . . F 4 28.022 -39.683 39.254 1 32.06 ? C2 GDP 202 A 1 
HETATM 26 N N2 GDP . . . F 4 28.358 -40.919 38.832 1 26.55 ? N2 GDP 202 A 1 
HETATM 27 N N3 GDP . . . F 4 27.058 -39.01 38.582 1 37.82 ? N3 GDP 202 A 1 
HETATM 28 C C4 GDP . . . F 4 26.69 -37.768 38.966 1 38.13 ? C4 GDP 202 A 1 
#
_model_server_stats.io_time_ms              80 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           282 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           28 
#