data_4EPR
#
_model_server_result.job_id            A6RUIurAX4ltILmiuwoMKA 
_model_server_result.datetime_utc      '2024-11-28 06:14:22' 
_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          4epr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":201}' 
#
_entry.id    4EPR 
#
_exptl.entry_id    4EPR 
_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         120 
_cell.entry_id            4EPR 
_cell.length_a            94.357 
_cell.length_b            94.357 
_cell.length_c            122.356 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4EPR 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        155 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_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    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 
#
_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 OG SER 18 A SER 17 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? 
metalc ? metalc2 B O2B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
metalc ? metalc3 C MG MG . A MG 202 1_555 D O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? 
metalc ? metalc4 C MG MG . A MG 202 1_555 D O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? 
metalc ? metalc5 C MG MG . A MG 202 1_555 D O HOH . A HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? 
metalc ? metalc6 C MG MG . A MG 202 1_555 D O HOH . A HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? 
#
_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                     4EPR 
_atom_sites.fract_transf_matrix[1][1]    0.010598 
_atom_sites.fract_transf_matrix[1][2]    0.006119 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012238 
_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]    0.008173 
_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 1 201 201 GDP GDP . 
C 3 MG A 1 202 202 MG MG . 
D 4 HOH A 1 301 301 HOH HOH . 
D 4 HOH A 2 302 302 HOH HOH . 
D 4 HOH A 3 303 303 HOH HOH . 
D 4 HOH A 4 304 304 HOH HOH . 
D 4 HOH A 5 305 305 HOH HOH . 
D 4 HOH A 6 306 306 HOH HOH . 
D 4 HOH A 7 307 307 HOH HOH . 
D 4 HOH A 8 308 308 HOH HOH . 
D 4 HOH A 9 309 309 HOH HOH . 
D 4 HOH A 10 310 310 HOH HOH . 
D 4 HOH A 11 311 311 HOH HOH . 
D 4 HOH A 12 312 312 HOH HOH . 
D 4 HOH A 13 313 313 HOH HOH . 
D 4 HOH A 14 314 314 HOH HOH . 
D 4 HOH A 15 315 315 HOH HOH . 
D 4 HOH A 16 316 316 HOH HOH . 
D 4 HOH A 17 317 317 HOH HOH . 
D 4 HOH A 18 318 318 HOH HOH . 
D 4 HOH A 19 319 319 HOH HOH . 
D 4 HOH A 20 320 320 HOH HOH . 
D 4 HOH A 21 321 321 HOH HOH . 
D 4 HOH A 22 322 322 HOH HOH . 
D 4 HOH A 23 323 323 HOH HOH . 
D 4 HOH A 24 324 324 HOH HOH . 
D 4 HOH A 25 325 325 HOH HOH . 
D 4 HOH A 26 326 326 HOH HOH . 
D 4 HOH A 27 327 327 HOH HOH . 
D 4 HOH A 28 328 328 HOH HOH . 
D 4 HOH A 29 329 329 HOH HOH . 
D 4 HOH A 30 330 330 HOH HOH . 
D 4 HOH A 31 331 331 HOH HOH . 
D 4 HOH A 32 332 332 HOH HOH . 
D 4 HOH A 33 333 333 HOH HOH . 
D 4 HOH A 34 334 334 HOH HOH . 
D 4 HOH A 35 335 335 HOH HOH . 
D 4 HOH A 36 336 336 HOH HOH . 
D 4 HOH A 37 337 337 HOH HOH . 
D 4 HOH A 38 338 338 HOH HOH . 
D 4 HOH A 39 339 339 HOH HOH . 
D 4 HOH A 40 340 340 HOH HOH . 
D 4 HOH A 41 341 341 HOH HOH . 
D 4 HOH A 42 342 342 HOH HOH . 
D 4 HOH A 43 343 343 HOH HOH . 
D 4 HOH A 44 344 344 HOH HOH . 
D 4 HOH A 45 345 345 HOH HOH . 
D 4 HOH A 46 346 346 HOH HOH . 
D 4 HOH A 47 347 347 HOH HOH . 
D 4 HOH A 48 348 348 HOH HOH . 
D 4 HOH A 49 349 349 HOH HOH . 
D 4 HOH A 50 350 350 HOH HOH . 
D 4 HOH A 51 351 351 HOH HOH . 
D 4 HOH A 52 352 352 HOH HOH . 
D 4 HOH A 53 353 353 HOH HOH . 
D 4 HOH A 54 354 354 HOH HOH . 
D 4 HOH A 55 355 355 HOH HOH . 
D 4 HOH A 56 356 356 HOH HOH . 
D 4 HOH A 57 357 357 HOH HOH . 
D 4 HOH A 58 358 358 HOH HOH . 
D 4 HOH A 59 359 359 HOH HOH . 
D 4 HOH A 60 360 360 HOH HOH . 
D 4 HOH A 61 361 361 HOH HOH . 
D 4 HOH A 62 362 362 HOH HOH . 
D 4 HOH A 63 363 363 HOH HOH . 
D 4 HOH A 64 364 364 HOH HOH . 
D 4 HOH A 65 365 365 HOH HOH . 
D 4 HOH A 66 366 366 HOH HOH . 
D 4 HOH A 67 367 367 HOH HOH . 
D 4 HOH A 68 368 368 HOH HOH . 
D 4 HOH A 69 369 369 HOH HOH . 
D 4 HOH A 70 370 370 HOH HOH . 
D 4 HOH A 71 371 371 HOH HOH . 
D 4 HOH A 72 372 372 HOH HOH . 
D 4 HOH A 73 373 373 HOH HOH . 
D 4 HOH A 74 374 374 HOH HOH . 
D 4 HOH A 75 375 375 HOH HOH . 
D 4 HOH A 76 376 376 HOH HOH . 
D 4 HOH A 77 377 377 HOH HOH . 
D 4 HOH A 78 378 378 HOH HOH . 
D 4 HOH A 79 379 379 HOH HOH . 
D 4 HOH A 80 380 380 HOH HOH . 
D 4 HOH A 81 381 381 HOH HOH . 
D 4 HOH A 82 382 382 HOH HOH . 
D 4 HOH A 83 383 383 HOH HOH . 
D 4 HOH A 84 384 384 HOH HOH . 
D 4 HOH A 85 385 385 HOH HOH . 
D 4 HOH A 86 386 386 HOH HOH . 
D 4 HOH A 87 387 387 HOH HOH . 
D 4 HOH A 88 388 388 HOH HOH . 
D 4 HOH A 89 389 389 HOH HOH . 
D 4 HOH A 90 390 390 HOH HOH . 
D 4 HOH A 91 391 392 HOH HOH . 
D 4 HOH A 92 392 393 HOH HOH . 
D 4 HOH A 93 393 394 HOH HOH . 
D 4 HOH A 94 394 395 HOH HOH . 
D 4 HOH A 95 395 396 HOH HOH . 
D 4 HOH A 96 396 397 HOH HOH . 
D 4 HOH A 97 397 398 HOH HOH . 
D 4 HOH A 98 398 399 HOH HOH . 
D 4 HOH A 99 399 400 HOH HOH . 
D 4 HOH A 100 400 401 HOH HOH . 
D 4 HOH A 101 401 402 HOH HOH . 
D 4 HOH A 102 402 403 HOH HOH . 
D 4 HOH A 103 403 404 HOH HOH . 
D 4 HOH A 104 404 405 HOH HOH . 
D 4 HOH A 105 405 406 HOH HOH . 
D 4 HOH A 106 406 407 HOH HOH . 
D 4 HOH A 107 407 408 HOH HOH . 
D 4 HOH A 108 408 409 HOH HOH . 
D 4 HOH A 109 409 410 HOH HOH . 
D 4 HOH A 110 410 411 HOH HOH . 
D 4 HOH A 111 411 412 HOH HOH . 
D 4 HOH A 112 412 413 HOH HOH . 
D 4 HOH A 113 413 414 HOH HOH . 
D 4 HOH A 114 414 415 HOH HOH . 
D 4 HOH A 115 415 416 HOH HOH . 
D 4 HOH A 116 416 417 HOH HOH . 
D 4 HOH A 117 417 418 HOH HOH . 
D 4 HOH A 118 418 419 HOH HOH . 
D 4 HOH A 119 419 420 HOH HOH . 
D 4 HOH A 120 420 421 HOH HOH . 
D 4 HOH A 121 421 422 HOH HOH . 
D 4 HOH A 122 422 423 HOH HOH . 
D 4 HOH A 123 423 424 HOH HOH . 
D 4 HOH A 124 424 425 HOH HOH . 
D 4 HOH A 125 425 426 HOH HOH . 
D 4 HOH A 126 426 427 HOH HOH . 
D 4 HOH A 127 427 428 HOH HOH . 
D 4 HOH A 128 428 429 HOH HOH . 
D 4 HOH A 129 429 430 HOH HOH . 
D 4 HOH A 130 430 431 HOH HOH . 
D 4 HOH A 131 431 432 HOH HOH . 
D 4 HOH A 132 432 433 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 -7.94 14.257 22.097 1 20.7 ? PB GDP 201 A 1 
HETATM 2 O O1B GDP . . . B 2 -6.958 14.283 23.202 1 19.4 ? O1B GDP 201 A 1 
HETATM 3 O O2B GDP . . . B 2 -8.393 15.609 21.393 1 21.83 ? O2B GDP 201 A 1 
HETATM 4 O O3B GDP . . . B 2 -7.385 13.353 20.91 1 20.29 ? O3B GDP 201 A 1 
HETATM 5 O O3A GDP . . . B 2 -9.197 13.583 22.78 1 16.63 ? O3A GDP 201 A 1 
HETATM 6 P PA GDP . . . B 2 -10.763 13.992 22.647 1 18 ? PA GDP 201 A 1 
HETATM 7 O O1A GDP . . . B 2 -11.075 15.32 23.175 1 19.68 ? O1A GDP 201 A 1 
HETATM 8 O O2A GDP . . . B 2 -11.054 13.69 21.248 1 21.34 ? O2A GDP 201 A 1 
HETATM 9 O O5' GDP . . . B 2 -11.388 12.897 23.549 1 19.39 ? O5' GDP 201 A 1 
HETATM 10 C C5' GDP . . . B 2 -11.135 11.466 23.317 1 22.16 ? C5' GDP 201 A 1 
HETATM 11 C C4' GDP . . . B 2 -12.378 10.759 23.75 1 19.9 ? C4' GDP 201 A 1 
HETATM 12 O O4' GDP . . . B 2 -12.439 10.704 25.183 1 17.99 ? O4' GDP 201 A 1 
HETATM 13 C C3' GDP . . . B 2 -13.693 11.43 23.27 1 22.89 ? C3' GDP 201 A 1 
HETATM 14 O O3' GDP . . . B 2 -14.58 10.308 23.089 1 24.74 ? O3' GDP 201 A 1 
HETATM 15 C C2' GDP . . . B 2 -14.171 12.177 24.507 1 24.94 ? C2' GDP 201 A 1 
HETATM 16 O O2' GDP . . . B 2 -15.569 12.041 24.683 1 30.32 ? O2' GDP 201 A 1 
HETATM 17 C C1' GDP . . . B 2 -13.648 11.329 25.676 1 19.03 ? C1' GDP 201 A 1 
HETATM 18 N N9 GDP . . . B 2 -13.228 12.274 26.82 1 17.62 ? N9 GDP 201 A 1 
HETATM 19 C C8 GDP . . . B 2 -12.489 13.383 26.771 1 16.84 ? C8 GDP 201 A 1 
HETATM 20 N N7 GDP . . . B 2 -12.348 13.845 28.003 1 16.95 ? N7 GDP 201 A 1 
HETATM 21 C C5 GDP . . . B 2 -13.076 13.053 28.857 1 16.61 ? C5 GDP 201 A 1 
HETATM 22 C C6 GDP . . . B 2 -13.345 13.035 30.223 1 12.6 ? C6 GDP 201 A 1 
HETATM 23 O O6 GDP . . . B 2 -12.916 13.895 31.012 1 13.82 ? O6 GDP 201 A 1 
HETATM 24 N N1 GDP . . . B 2 -14.12 11.995 30.776 1 13.08 ? N1 GDP 201 A 1 
HETATM 25 C C2 GDP . . . B 2 -14.68 10.991 29.911 1 17.29 ? C2 GDP 201 A 1 
HETATM 26 N N2 GDP . . . B 2 -15.445 10.004 30.403 1 15.03 ? N2 GDP 201 A 1 
HETATM 27 N N3 GDP . . . B 2 -14.371 11.043 28.605 1 17.69 ? N3 GDP 201 A 1 
HETATM 28 C C4 GDP . . . B 2 -13.613 12.042 28.089 1 16.09 ? C4 GDP 201 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           396 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           28 
#