data_6N2J
#
_model_server_result.job_id            0dZXb4QOwdyfyh_XYAKrdQ 
_model_server_result.datetime_utc      '2024-12-04 16:21:51' 
_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          6n2j 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":201}' 
#
_entry.id    6N2J 
#
_exptl.entry_id    6N2J 
_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            6N2J 
_cell.length_a            40.25 
_cell.length_b            51.13 
_cell.length_c            90.12 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6N2J 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_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,E 
_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
covale ? covale1 A SG CYS 13 A CYS 12 1_555 D C30 K9M . A K9M 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.718 ? 
metalc ? metalc1 A OG SER 18 A SER 17 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? 
metalc ? metalc2 B O2B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? 
metalc ? metalc3 C MG MG . A MG 202 1_555 E O HOH . A HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? 
metalc ? metalc4 C MG MG . A MG 202 1_555 E O HOH . A HOH 325 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? 
metalc ? metalc5 C MG MG . A MG 202 1_555 E O HOH . A HOH 343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? 
metalc ? metalc6 C MG MG . A MG 202 1_555 E O HOH . A HOH 374 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? 
#
_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                     6N2J 
_atom_sites.fract_transf_matrix[1][1]    0.024845 
_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]    0.019558 
_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]    0.011096 
_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 K9M A 1 203 1 K9M SM1 . 
E 5 HOH A 1 301 42 HOH HOH . 
E 5 HOH A 2 302 120 HOH HOH . 
E 5 HOH A 3 303 116 HOH HOH . 
E 5 HOH A 4 304 104 HOH HOH . 
E 5 HOH A 5 305 13 HOH HOH . 
E 5 HOH A 6 306 109 HOH HOH . 
E 5 HOH A 7 307 110 HOH HOH . 
E 5 HOH A 8 308 22 HOH HOH . 
E 5 HOH A 9 309 33 HOH HOH . 
E 5 HOH A 10 310 59 HOH HOH . 
E 5 HOH A 11 311 57 HOH HOH . 
E 5 HOH A 12 312 1 HOH HOH . 
E 5 HOH A 13 313 85 HOH HOH . 
E 5 HOH A 14 314 47 HOH HOH . 
E 5 HOH A 15 315 69 HOH HOH . 
E 5 HOH A 16 316 80 HOH HOH . 
E 5 HOH A 17 317 31 HOH HOH . 
E 5 HOH A 18 318 78 HOH HOH . 
E 5 HOH A 19 319 52 HOH HOH . 
E 5 HOH A 20 320 16 HOH HOH . 
E 5 HOH A 21 321 37 HOH HOH . 
E 5 HOH A 22 322 45 HOH HOH . 
E 5 HOH A 23 323 82 HOH HOH . 
E 5 HOH A 24 324 24 HOH HOH . 
E 5 HOH A 25 325 65 HOH HOH . 
E 5 HOH A 26 326 84 HOH HOH . 
E 5 HOH A 27 327 6 HOH HOH . 
E 5 HOH A 28 328 114 HOH HOH . 
E 5 HOH A 29 329 86 HOH HOH . 
E 5 HOH A 30 330 100 HOH HOH . 
E 5 HOH A 31 331 34 HOH HOH . 
E 5 HOH A 32 332 105 HOH HOH . 
E 5 HOH A 33 333 112 HOH HOH . 
E 5 HOH A 34 334 121 HOH HOH . 
E 5 HOH A 35 335 8 HOH HOH . 
E 5 HOH A 36 336 102 HOH HOH . 
E 5 HOH A 37 337 17 HOH HOH . 
E 5 HOH A 38 338 94 HOH HOH . 
E 5 HOH A 39 339 76 HOH HOH . 
E 5 HOH A 40 340 81 HOH HOH . 
E 5 HOH A 41 341 60 HOH HOH . 
E 5 HOH A 42 342 106 HOH HOH . 
E 5 HOH A 43 343 66 HOH HOH . 
E 5 HOH A 44 344 95 HOH HOH . 
E 5 HOH A 45 345 20 HOH HOH . 
E 5 HOH A 46 346 30 HOH HOH . 
E 5 HOH A 47 347 99 HOH HOH . 
E 5 HOH A 48 348 25 HOH HOH . 
E 5 HOH A 49 349 115 HOH HOH . 
E 5 HOH A 50 350 55 HOH HOH . 
E 5 HOH A 51 351 83 HOH HOH . 
E 5 HOH A 52 352 41 HOH HOH . 
E 5 HOH A 53 353 61 HOH HOH . 
E 5 HOH A 54 354 74 HOH HOH . 
E 5 HOH A 55 355 122 HOH HOH . 
E 5 HOH A 56 356 18 HOH HOH . 
E 5 HOH A 57 357 46 HOH HOH . 
E 5 HOH A 58 358 19 HOH HOH . 
E 5 HOH A 59 359 93 HOH HOH . 
E 5 HOH A 60 360 39 HOH HOH . 
E 5 HOH A 61 361 4 HOH HOH . 
E 5 HOH A 62 362 15 HOH HOH . 
E 5 HOH A 63 363 63 HOH HOH . 
E 5 HOH A 64 364 70 HOH HOH . 
E 5 HOH A 65 365 92 HOH HOH . 
E 5 HOH A 66 366 90 HOH HOH . 
E 5 HOH A 67 367 108 HOH HOH . 
E 5 HOH A 68 368 36 HOH HOH . 
E 5 HOH A 69 369 48 HOH HOH . 
E 5 HOH A 70 370 111 HOH HOH . 
E 5 HOH A 71 371 5 HOH HOH . 
E 5 HOH A 72 372 28 HOH HOH . 
E 5 HOH A 73 373 53 HOH HOH . 
E 5 HOH A 74 374 67 HOH HOH . 
E 5 HOH A 75 375 11 HOH HOH . 
E 5 HOH A 76 376 79 HOH HOH . 
E 5 HOH A 77 377 14 HOH HOH . 
E 5 HOH A 78 378 12 HOH HOH . 
E 5 HOH A 79 379 9 HOH HOH . 
E 5 HOH A 80 380 7 HOH HOH . 
E 5 HOH A 81 381 56 HOH HOH . 
E 5 HOH A 82 382 21 HOH HOH . 
E 5 HOH A 83 383 2 HOH HOH . 
E 5 HOH A 84 384 29 HOH HOH . 
E 5 HOH A 85 385 113 HOH HOH . 
E 5 HOH A 86 386 88 HOH HOH . 
E 5 HOH A 87 387 101 HOH HOH . 
E 5 HOH A 88 388 75 HOH HOH . 
E 5 HOH A 89 389 50 HOH HOH . 
E 5 HOH A 90 390 23 HOH HOH . 
E 5 HOH A 91 391 3 HOH HOH . 
E 5 HOH A 92 392 43 HOH HOH . 
E 5 HOH A 93 393 26 HOH HOH . 
E 5 HOH A 94 394 103 HOH HOH . 
E 5 HOH A 95 395 27 HOH HOH . 
E 5 HOH A 96 396 40 HOH HOH . 
E 5 HOH A 97 397 44 HOH HOH . 
E 5 HOH A 98 398 72 HOH HOH . 
E 5 HOH A 99 399 117 HOH HOH . 
E 5 HOH A 100 400 35 HOH HOH . 
E 5 HOH A 101 401 73 HOH HOH . 
E 5 HOH A 102 402 68 HOH HOH . 
E 5 HOH A 103 403 58 HOH HOH . 
E 5 HOH A 104 404 87 HOH HOH . 
E 5 HOH A 105 405 119 HOH HOH . 
E 5 HOH A 106 406 38 HOH HOH . 
E 5 HOH A 107 407 10 HOH HOH . 
E 5 HOH A 108 408 107 HOH HOH . 
E 5 HOH A 109 409 89 HOH HOH . 
E 5 HOH A 110 410 54 HOH HOH . 
E 5 HOH A 111 411 71 HOH HOH . 
E 5 HOH A 112 412 62 HOH HOH . 
E 5 HOH A 113 413 118 HOH HOH . 
E 5 HOH A 114 414 91 HOH HOH . 
E 5 HOH A 115 415 96 HOH HOH . 
E 5 HOH A 116 416 97 HOH HOH . 
E 5 HOH A 117 417 77 HOH HOH . 
E 5 HOH A 118 418 49 HOH HOH . 
E 5 HOH A 119 419 51 HOH HOH . 
E 5 HOH A 120 420 98 HOH HOH . 
E 5 HOH A 121 421 32 HOH HOH . 
E 5 HOH A 122 422 64 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 28.276 -3.272 -15.812 1 22.39 ? PB GDP 201 A 1 
HETATM 2 O O1B GDP . . . B 2 29.233 -2.644 -16.823 1 22.08 ? O1B GDP 201 A 1 
HETATM 3 O O2B GDP . . . B 2 27.598 -4.549 -16.301 1 20.05 ? O2B GDP 201 A 1 
HETATM 4 O O3B GDP . . . B 2 27.336 -2.192 -15.243 1 21.28 ? O3B GDP 201 A 1 
HETATM 5 O O3A GDP . . . B 2 29.201 -3.703 -14.543 1 22.19 ? O3A GDP 201 A 1 
HETATM 6 P PA GDP . . . B 2 29.784 -5.201 -14.23 1 24.05 ? PA GDP 201 A 1 
HETATM 7 O O1A GDP . . . B 2 30.48 -5.695 -15.481 1 25.56 ? O1A GDP 201 A 1 
HETATM 8 O O2A GDP . . . B 2 28.754 -6.019 -13.527 1 21.17 ? O2A GDP 201 A 1 
HETATM 9 O O5' GDP . . . B 2 30.81 -4.831 -13.053 1 22.78 ? O5' GDP 201 A 1 
HETATM 10 C C5' GDP . . . B 2 31.927 -3.978 -13.325 1 20.53 ? C5' GDP 201 A 1 
HETATM 11 C C4' GDP . . . B 2 33.042 -4.391 -12.361 1 26.51 ? C4' GDP 201 A 1 
HETATM 12 O O4' GDP . . . B 2 32.693 -4.045 -11.024 1 26.97 ? O4' GDP 201 A 1 
HETATM 13 C C3' GDP . . . B 2 33.302 -5.915 -12.353 1 28.3 ? C3' GDP 201 A 1 
HETATM 14 O O3' GDP . . . B 2 34.667 -6.227 -12.203 1 29.77 ? O3' GDP 201 A 1 
HETATM 15 C C2' GDP . . . B 2 32.537 -6.419 -11.143 1 24.34 ? C2' GDP 201 A 1 
HETATM 16 O O2' GDP . . . B 2 33.053 -7.59 -10.524 1 28.25 ? O2' GDP 201 A 1 
HETATM 17 C C1' GDP . . . B 2 32.656 -5.239 -10.202 1 24.76 ? C1' GDP 201 A 1 
HETATM 18 N N9 GDP . . . B 2 31.473 -5.137 -9.319 1 24.19 ? N9 GDP 201 A 1 
HETATM 19 C C8 GDP . . . B 2 30.148 -5.152 -9.692 1 23.23 ? C8 GDP 201 A 1 
HETATM 20 N N7 GDP . . . B 2 29.375 -4.952 -8.61 1 22.94 ? N7 GDP 201 A 1 
HETATM 21 C C5 GDP . . . B 2 30.234 -4.791 -7.581 1 23.64 ? C5 GDP 201 A 1 
HETATM 22 C C6 GDP . . . B 2 30.064 -4.51 -6.158 1 23.23 ? C6 GDP 201 A 1 
HETATM 23 O O6 GDP . . . B 2 28.946 -4.416 -5.608 1 23.91 ? O6 GDP 201 A 1 
HETATM 24 N N1 GDP . . . B 2 31.142 -4.416 -5.44 1 25.13 ? N1 GDP 201 A 1 
HETATM 25 C C2 GDP . . . B 2 32.388 -4.535 -5.896 1 26.81 ? C2 GDP 201 A 1 
HETATM 26 N N2 GDP . . . B 2 33.38 -4.404 -5.004 1 27.56 ? N2 GDP 201 A 1 
HETATM 27 N N3 GDP . . . B 2 32.635 -4.748 -7.189 1 21.47 ? N3 GDP 201 A 1 
HETATM 28 C C4 GDP . . . B 2 31.585 -4.903 -8.044 1 23.58 ? C4 GDP 201 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           46 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           281 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           28 
#