data_3LRP
#
_model_server_result.job_id            SVQqbjlGMfdild1_XSgyNw 
_model_server_result.datetime_utc      '2024-11-15 11:23:19' 
_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          3lrp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":182}' 
#
_entry.id    3LRP 
#
_exptl.entry_id    3LRP 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          2 
_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            3LRP 
_cell.length_a            45.732 
_cell.length_b            147.28 
_cell.length_c            64.229 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3LRP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 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 
PISA dimeric 2 software_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,C,D,E 1 1 
A,B,C,D,E 2 1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 45.732 0 32.1145 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_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 31 A THR 31 1_555 C MG MG . A MG 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? 
metalc ? metalc2 B O2B GDP . A GDP 182 1_555 C MG MG . A MG 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? 
metalc ? metalc3 C MG MG . A MG 183 1_555 E O HOH . A HOH 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.887 ? 
metalc ? metalc4 C MG MG . A MG 183 1_555 E O HOH . A HOH 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? 
metalc ? metalc5 C MG MG . A MG 183 1_555 E O HOH . A HOH 290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? 
#
_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                     3LRP 
_atom_sites.fract_transf_matrix[1][1]    0.021867 
_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]    0.00679 
_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]    0.015569 
_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
B 2 GDP A 1 182 182 GDP GDP . 
C 3 MG A 1 183 183 MG MG . 
D 4 SO4 A 1 184 184 SO4 SO4 . 
E 5 HOH A 1 201 201 HOH HOH . 
E 5 HOH A 2 202 202 HOH HOH . 
E 5 HOH A 3 203 203 HOH HOH . 
E 5 HOH A 4 204 204 HOH HOH . 
E 5 HOH A 5 205 205 HOH HOH . 
E 5 HOH A 6 206 206 HOH HOH . 
E 5 HOH A 7 207 207 HOH HOH . 
E 5 HOH A 8 208 208 HOH HOH . 
E 5 HOH A 9 209 209 HOH HOH . 
E 5 HOH A 10 210 210 HOH HOH . 
E 5 HOH A 11 211 211 HOH HOH . 
E 5 HOH A 12 212 212 HOH HOH . 
E 5 HOH A 13 213 213 HOH HOH . 
E 5 HOH A 14 214 214 HOH HOH . 
E 5 HOH A 15 215 215 HOH HOH . 
E 5 HOH A 16 216 216 HOH HOH . 
E 5 HOH A 17 217 217 HOH HOH . 
E 5 HOH A 18 218 218 HOH HOH . 
E 5 HOH A 19 219 219 HOH HOH . 
E 5 HOH A 20 220 220 HOH HOH . 
E 5 HOH A 21 221 221 HOH HOH . 
E 5 HOH A 22 222 222 HOH HOH . 
E 5 HOH A 23 223 223 HOH HOH . 
E 5 HOH A 24 224 224 HOH HOH . 
E 5 HOH A 25 225 225 HOH HOH . 
E 5 HOH A 26 226 226 HOH HOH . 
E 5 HOH A 27 227 227 HOH HOH . 
E 5 HOH A 28 228 228 HOH HOH . 
E 5 HOH A 29 229 229 HOH HOH . 
E 5 HOH A 30 230 230 HOH HOH . 
E 5 HOH A 31 231 231 HOH HOH . 
E 5 HOH A 32 232 232 HOH HOH . 
E 5 HOH A 33 233 233 HOH HOH . 
E 5 HOH A 34 234 234 HOH HOH . 
E 5 HOH A 35 235 235 HOH HOH . 
E 5 HOH A 36 236 236 HOH HOH . 
E 5 HOH A 37 237 237 HOH HOH . 
E 5 HOH A 38 238 238 HOH HOH . 
E 5 HOH A 39 239 239 HOH HOH . 
E 5 HOH A 40 240 240 HOH HOH . 
E 5 HOH A 41 241 241 HOH HOH . 
E 5 HOH A 42 242 242 HOH HOH . 
E 5 HOH A 43 243 243 HOH HOH . 
E 5 HOH A 44 244 244 HOH HOH . 
E 5 HOH A 45 245 245 HOH HOH . 
E 5 HOH A 46 246 246 HOH HOH . 
E 5 HOH A 47 247 247 HOH HOH . 
E 5 HOH A 48 248 248 HOH HOH . 
E 5 HOH A 49 249 249 HOH HOH . 
E 5 HOH A 50 250 250 HOH HOH . 
E 5 HOH A 51 251 251 HOH HOH . 
E 5 HOH A 52 252 252 HOH HOH . 
E 5 HOH A 53 253 253 HOH HOH . 
E 5 HOH A 54 254 254 HOH HOH . 
E 5 HOH A 55 255 255 HOH HOH . 
E 5 HOH A 56 256 256 HOH HOH . 
E 5 HOH A 57 257 257 HOH HOH . 
E 5 HOH A 58 258 258 HOH HOH . 
E 5 HOH A 59 259 259 HOH HOH . 
E 5 HOH A 60 260 260 HOH HOH . 
E 5 HOH A 61 261 261 HOH HOH . 
E 5 HOH A 62 262 262 HOH HOH . 
E 5 HOH A 63 263 263 HOH HOH . 
E 5 HOH A 64 264 264 HOH HOH . 
E 5 HOH A 65 265 265 HOH HOH . 
E 5 HOH A 66 266 266 HOH HOH . 
E 5 HOH A 67 267 267 HOH HOH . 
E 5 HOH A 68 268 268 HOH HOH . 
E 5 HOH A 69 269 269 HOH HOH . 
E 5 HOH A 70 270 270 HOH HOH . 
E 5 HOH A 71 271 271 HOH HOH . 
E 5 HOH A 72 272 272 HOH HOH . 
E 5 HOH A 73 273 273 HOH HOH . 
E 5 HOH A 74 274 274 HOH HOH . 
E 5 HOH A 75 275 275 HOH HOH . 
E 5 HOH A 76 276 276 HOH HOH . 
E 5 HOH A 77 277 277 HOH HOH . 
E 5 HOH A 78 278 278 HOH HOH . 
E 5 HOH A 79 279 279 HOH HOH . 
E 5 HOH A 80 280 280 HOH HOH . 
E 5 HOH A 81 281 281 HOH HOH . 
E 5 HOH A 82 282 282 HOH HOH . 
E 5 HOH A 83 283 283 HOH HOH . 
E 5 HOH A 84 284 284 HOH HOH . 
E 5 HOH A 85 285 285 HOH HOH . 
E 5 HOH A 86 286 286 HOH HOH . 
E 5 HOH A 87 287 287 HOH HOH . 
E 5 HOH A 88 288 288 HOH HOH . 
E 5 HOH A 89 289 289 HOH HOH . 
E 5 HOH A 90 290 290 HOH HOH . 
E 5 HOH A 91 291 291 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 . . . B 2 20.288 49.937 12.417 1 20.33 ? PB GDP 182 A 1 
HETATM 2 O O1B GDP . . . B 2 20.173 49.563 11.004 1 23.42 ? O1B GDP 182 A 1 
HETATM 3 O O2B GDP . . . B 2 19.69 51.224 12.77 1 22.62 ? O2B GDP 182 A 1 
HETATM 4 O O3B GDP . . . B 2 19.731 48.93 13.346 1 24.5 ? O3B GDP 182 A 1 
HETATM 5 O O3A GDP . . . B 2 21.86 50.104 12.748 1 25.43 ? O3A GDP 182 A 1 
HETATM 6 P PA GDP . . . B 2 22.756 51.472 12.772 1 28.29 ? PA GDP 182 A 1 
HETATM 7 O O1A GDP . . . B 2 23.623 51.808 11.65 1 28.94 ? O1A GDP 182 A 1 
HETATM 8 O O2A GDP . . . B 2 22.947 51.984 14.148 1 28.65 ? O2A GDP 182 A 1 
HETATM 9 O O5' GDP . . . B 2 23.892 50.402 13.207 1 28.69 ? O5' GDP 182 A 1 
HETATM 10 C C5' GDP . . . B 2 24.443 49.35 12.376 1 22.39 ? C5' GDP 182 A 1 
HETATM 11 C C4' GDP . . . B 2 25.891 49.025 12.75 1 21.74 ? C4' GDP 182 A 1 
HETATM 12 O O4' GDP . . . B 2 26.642 48.846 11.525 1 19.74 ? O4' GDP 182 A 1 
HETATM 13 C C3' GDP . . . B 2 26.627 50.109 13.514 1 18.71 ? C3' GDP 182 A 1 
HETATM 14 O O3' GDP . . . B 2 27.577 49.374 14.303 1 17.91 ? O3' GDP 182 A 1 
HETATM 15 C C2' GDP . . . B 2 27.261 50.932 12.361 1 19.45 ? C2' GDP 182 A 1 
HETATM 16 O O2' GDP . . . B 2 28.441 51.676 12.785 1 19.88 ? O2' GDP 182 A 1 
HETATM 17 C C1' GDP . . . B 2 27.619 49.865 11.342 1 15.75 ? C1' GDP 182 A 1 
HETATM 18 N N9 GDP . . . B 2 27.504 50.333 9.938 1 21.83 ? N9 GDP 182 A 1 
HETATM 19 C C8 GDP . . . B 2 26.523 51.097 9.316 1 20 ? C8 GDP 182 A 1 
HETATM 20 N N7 GDP . . . B 2 26.733 51.328 8.038 1 20.99 ? N7 GDP 182 A 1 
HETATM 21 C C5 GDP . . . B 2 27.936 50.668 7.804 1 20.78 ? C5 GDP 182 A 1 
HETATM 22 C C6 GDP . . . B 2 28.717 50.525 6.633 1 20.74 ? C6 GDP 182 A 1 
HETATM 23 O O6 GDP . . . B 2 28.49 50.98 5.504 1 16.28 ? O6 GDP 182 A 1 
HETATM 24 N N1 GDP . . . B 2 29.868 49.776 6.821 1 21.61 ? N1 GDP 182 A 1 
HETATM 25 C C2 GDP . . . B 2 30.26 49.2 8.028 1 23.35 ? C2 GDP 182 A 1 
HETATM 26 N N2 GDP . . . B 2 31.39 48.507 8.06 1 23.55 ? N2 GDP 182 A 1 
HETATM 27 N N3 GDP . . . B 2 29.544 49.32 9.146 1 22.32 ? N3 GDP 182 A 1 
HETATM 28 C C4 GDP . . . B 2 28.408 50.056 8.973 1 22.43 ? C4 GDP 182 A 1 
#
_model_server_stats.io_time_ms              47 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           320 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           28 
#