data_6VJJ
#
_model_server_result.job_id            r0Rf1NtiB2tDwfhHehiD7g 
_model_server_result.datetime_utc      '2024-11-02 12:17:43' 
_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          6vjj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":202}' 
#
_entry.id    6VJJ 
#
_exptl.entry_id    6VJJ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              522.196 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' 
_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            6VJJ 
_cell.length_a            44.132 
_cell.length_b            67.572 
_cell.length_c            71.26 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6VJJ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 2 21 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L 
_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                      4 
_struct_asym.id                             D 
_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 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? 
metalc ? metalc2 A OG1 THR 36 A THR 35 1_555 C MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
metalc ? metalc3 C MG MG . A MG 201 1_555 D O2G GNP . A GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
metalc ? metalc4 C MG MG . A MG 201 1_555 D O2B GNP . A GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc5 C MG MG . A MG 201 1_555 K O HOH . A HOH 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? 
metalc ? metalc6 C MG MG . A MG 201 1_555 K O HOH . A HOH 325 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
#
_chem_comp.formula           'C10 H17 N6 O13 P3' 
_chem_comp.formula_weight    522.196 
_chem_comp.id                GNP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' 
_chem_comp.type              non-polymer 
_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
PG O1G GNP doub 138 n n 
PG O2G GNP sing 139 n n 
PG O3G GNP sing 140 n n 
PG N3B GNP sing 141 n n 
O2G HOG2 GNP sing 142 n n 
O3G HOG3 GNP sing 143 n n 
N3B PB GNP sing 144 n n 
N3B HNB3 GNP sing 145 n n 
PB O1B GNP doub 146 n n 
PB O2B GNP sing 147 n n 
PB O3A GNP sing 148 n n 
O2B HOB2 GNP sing 149 n n 
O3A PA GNP sing 150 n n 
PA O1A GNP doub 151 n n 
PA O2A GNP sing 152 n n 
PA O5' GNP sing 153 n n 
O2A HOA2 GNP sing 154 n n 
O5' C5' GNP sing 155 n n 
C5' C4' GNP sing 156 n n 
C5' "H5'2" GNP sing 157 n n 
C5' "H5'1" GNP sing 158 n n 
C4' O4' GNP sing 159 n n 
C4' C3' GNP sing 160 n n 
C4' H4' GNP sing 161 n n 
O4' C1' GNP sing 162 n n 
C3' O3' GNP sing 163 n n 
C3' C2' GNP sing 164 n n 
C3' H3' GNP sing 165 n n 
O3' HO3' GNP sing 166 n n 
C2' O2' GNP sing 167 n n 
C2' C1' GNP sing 168 n n 
C2' H2' GNP sing 169 n n 
O2' HO2' GNP sing 170 n n 
C1' N9 GNP sing 171 n n 
C1' H1' GNP sing 172 n n 
N9 C8 GNP sing 173 n y 
N9 C4 GNP sing 174 n y 
C8 N7 GNP doub 175 n y 
C8 H8 GNP sing 176 n n 
N7 C5 GNP sing 177 n y 
C5 C6 GNP sing 178 n y 
C5 C4 GNP doub 179 n y 
C6 O6 GNP doub 180 n n 
C6 N1 GNP sing 181 n y 
N1 C2 GNP sing 182 n y 
N1 HN1 GNP sing 183 n n 
C2 N2 GNP sing 184 n n 
C2 N3 GNP doub 185 n y 
N2 HN21 GNP sing 186 n n 
N2 HN22 GNP sing 187 n n 
N3 C4 GNP sing 188 n y 
#
_atom_sites.entry_id                     6VJJ 
_atom_sites.fract_transf_matrix[1][1]    0.022659 
_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]    0.014799 
_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]    0.014033 
_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
C 3 MG A 1 201 1 MG MG . 
D 4 GNP A 1 202 2 GNP GNP . 
E 5 CL A 1 203 3 CL CL . 
F 5 CL A 1 204 4 CL CL . 
G 5 CL A 1 205 5 CL CL . 
H 6 EDO A 1 206 6 EDO EDO . 
I 7 MPD A 1 207 8 MPD MPD . 
J 6 EDO B 1 201 7 EDO EDO . 
K 8 HOH A 1 301 46 HOH HOH . 
K 8 HOH A 2 302 124 HOH HOH . 
K 8 HOH A 3 303 95 HOH HOH . 
K 8 HOH A 4 304 31 HOH HOH . 
K 8 HOH A 5 305 23 HOH HOH . 
K 8 HOH A 6 306 134 HOH HOH . 
K 8 HOH A 7 307 96 HOH HOH . 
K 8 HOH A 8 308 68 HOH HOH . 
K 8 HOH A 9 309 63 HOH HOH . 
K 8 HOH A 10 310 71 HOH HOH . 
K 8 HOH A 11 311 76 HOH HOH . 
K 8 HOH A 12 312 126 HOH HOH . 
K 8 HOH A 13 313 22 HOH HOH . 
K 8 HOH A 14 314 58 HOH HOH . 
K 8 HOH A 15 315 77 HOH HOH . 
K 8 HOH A 16 316 9 HOH HOH . 
K 8 HOH A 17 317 97 HOH HOH . 
K 8 HOH A 18 318 10 HOH HOH . 
K 8 HOH A 19 319 1 HOH HOH . 
K 8 HOH A 20 320 18 HOH HOH . 
K 8 HOH A 21 321 73 HOH HOH . 
K 8 HOH A 22 322 121 HOH HOH . 
K 8 HOH A 23 323 108 HOH HOH . 
K 8 HOH A 24 324 81 HOH HOH . 
K 8 HOH A 25 325 4 HOH HOH . 
K 8 HOH A 26 326 11 HOH HOH . 
K 8 HOH A 27 327 6 HOH HOH . 
K 8 HOH A 28 328 2 HOH HOH . 
K 8 HOH A 29 329 41 HOH HOH . 
K 8 HOH A 30 330 38 HOH HOH . 
K 8 HOH A 31 331 111 HOH HOH . 
K 8 HOH A 32 332 140 HOH HOH . 
K 8 HOH A 33 333 48 HOH HOH . 
K 8 HOH A 34 334 40 HOH HOH . 
K 8 HOH A 35 335 99 HOH HOH . 
K 8 HOH A 36 336 3 HOH HOH . 
K 8 HOH A 37 337 93 HOH HOH . 
K 8 HOH A 38 338 65 HOH HOH . 
K 8 HOH A 39 339 80 HOH HOH . 
K 8 HOH A 40 340 15 HOH HOH . 
K 8 HOH A 41 341 119 HOH HOH . 
K 8 HOH A 42 342 67 HOH HOH . 
K 8 HOH A 43 343 90 HOH HOH . 
K 8 HOH A 44 344 104 HOH HOH . 
K 8 HOH A 45 345 44 HOH HOH . 
K 8 HOH A 46 346 100 HOH HOH . 
K 8 HOH A 47 347 56 HOH HOH . 
K 8 HOH A 48 348 42 HOH HOH . 
K 8 HOH A 49 349 12 HOH HOH . 
K 8 HOH A 50 350 61 HOH HOH . 
K 8 HOH A 51 351 53 HOH HOH . 
K 8 HOH A 52 352 14 HOH HOH . 
K 8 HOH A 53 353 83 HOH HOH . 
K 8 HOH A 54 354 5 HOH HOH . 
K 8 HOH A 55 355 7 HOH HOH . 
K 8 HOH A 56 356 84 HOH HOH . 
K 8 HOH A 57 357 89 HOH HOH . 
K 8 HOH A 58 358 28 HOH HOH . 
K 8 HOH A 59 359 59 HOH HOH . 
K 8 HOH A 60 360 127 HOH HOH . 
K 8 HOH A 61 361 137 HOH HOH . 
K 8 HOH A 62 362 110 HOH HOH . 
K 8 HOH A 63 363 64 HOH HOH . 
K 8 HOH A 64 364 114 HOH HOH . 
K 8 HOH A 65 365 129 HOH HOH . 
K 8 HOH A 66 366 29 HOH HOH . 
K 8 HOH A 67 367 109 HOH HOH . 
K 8 HOH A 68 368 85 HOH HOH . 
K 8 HOH A 69 369 45 HOH HOH . 
K 8 HOH A 70 370 79 HOH HOH . 
K 8 HOH A 71 371 94 HOH HOH . 
K 8 HOH A 72 372 117 HOH HOH . 
K 8 HOH A 73 373 55 HOH HOH . 
K 8 HOH A 74 374 26 HOH HOH . 
K 8 HOH A 75 375 27 HOH HOH . 
K 8 HOH A 76 376 142 HOH HOH . 
K 8 HOH A 77 377 107 HOH HOH . 
K 8 HOH A 78 378 143 HOH HOH . 
K 8 HOH A 79 379 105 HOH HOH . 
K 8 HOH A 80 380 132 HOH HOH . 
K 8 HOH A 81 381 113 HOH HOH . 
K 8 HOH A 82 382 106 HOH HOH . 
K 8 HOH A 83 383 130 HOH HOH . 
K 8 HOH A 84 384 112 HOH HOH . 
K 8 HOH A 85 385 101 HOH HOH . 
K 8 HOH A 86 386 25 HOH HOH . 
K 8 HOH A 87 387 135 HOH HOH . 
K 8 HOH A 88 388 139 HOH HOH . 
K 8 HOH A 89 389 125 HOH HOH . 
K 8 HOH A 90 390 118 HOH HOH . 
L 8 HOH B 1 301 35 HOH HOH . 
L 8 HOH B 2 302 141 HOH HOH . 
L 8 HOH B 3 303 122 HOH HOH . 
L 8 HOH B 4 304 49 HOH HOH . 
L 8 HOH B 5 305 8 HOH HOH . 
L 8 HOH B 6 306 92 HOH HOH . 
L 8 HOH B 7 307 52 HOH HOH . 
L 8 HOH B 8 308 33 HOH HOH . 
L 8 HOH B 9 309 37 HOH HOH . 
L 8 HOH B 10 310 69 HOH HOH . 
L 8 HOH B 11 311 20 HOH HOH . 
L 8 HOH B 12 312 57 HOH HOH . 
L 8 HOH B 13 313 19 HOH HOH . 
L 8 HOH B 14 314 50 HOH HOH . 
L 8 HOH B 15 315 17 HOH HOH . 
L 8 HOH B 16 316 47 HOH HOH . 
L 8 HOH B 17 317 13 HOH HOH . 
L 8 HOH B 18 318 87 HOH HOH . 
L 8 HOH B 19 319 102 HOH HOH . 
L 8 HOH B 20 320 21 HOH HOH . 
L 8 HOH B 21 321 39 HOH HOH . 
L 8 HOH B 22 322 75 HOH HOH . 
L 8 HOH B 23 323 34 HOH HOH . 
L 8 HOH B 24 324 115 HOH HOH . 
L 8 HOH B 25 325 32 HOH HOH . 
L 8 HOH B 26 326 74 HOH HOH . 
L 8 HOH B 27 327 116 HOH HOH . 
L 8 HOH B 28 328 60 HOH HOH . 
L 8 HOH B 29 329 43 HOH HOH . 
L 8 HOH B 30 330 78 HOH HOH . 
L 8 HOH B 31 331 30 HOH HOH . 
L 8 HOH B 32 332 51 HOH HOH . 
L 8 HOH B 33 333 91 HOH HOH . 
L 8 HOH B 34 334 16 HOH HOH . 
L 8 HOH B 35 335 66 HOH HOH . 
L 8 HOH B 36 336 131 HOH HOH . 
L 8 HOH B 37 337 24 HOH HOH . 
L 8 HOH B 38 338 72 HOH HOH . 
L 8 HOH B 39 339 133 HOH HOH . 
L 8 HOH B 40 340 36 HOH HOH . 
L 8 HOH B 41 341 82 HOH HOH . 
L 8 HOH B 42 342 62 HOH HOH . 
L 8 HOH B 43 343 54 HOH HOH . 
L 8 HOH B 44 344 103 HOH HOH . 
L 8 HOH B 45 345 123 HOH HOH . 
L 8 HOH B 46 346 88 HOH HOH . 
L 8 HOH B 47 347 144 HOH HOH . 
L 8 HOH B 48 348 98 HOH HOH . 
L 8 HOH B 49 349 145 HOH HOH . 
L 8 HOH B 50 350 120 HOH HOH . 
L 8 HOH B 51 351 136 HOH HOH . 
L 8 HOH B 52 352 138 HOH HOH . 
L 8 HOH B 53 353 128 HOH HOH . 
L 8 HOH B 54 354 86 HOH HOH . 
L 8 HOH B 55 355 70 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 PG GNP . . . D 4 -9.114 -16.362 14.515 1 11.41 ? PG GNP 202 A 1 
HETATM 2 O O1G GNP . . . D 4 -7.982 -17.304 14.276 1 12.64 ? O1G GNP 202 A 1 
HETATM 3 O O2G GNP . . . D 4 -9.265 -16.102 16.004 1 11.88 ? O2G GNP 202 A 1 
HETATM 4 O O3G GNP . . . D 4 -10.419 -16.875 13.893 1 13.41 ? O3G GNP 202 A 1 
HETATM 5 N N3B GNP . . . D 4 -8.704 -14.901 13.724 1 10.97 ? N3B GNP 202 A 1 
HETATM 6 P PB GNP . . . D 4 -9.544 -13.506 13.899 1 10.47 ? PB GNP 202 A 1 
HETATM 7 O O1B GNP . . . D 4 -10.783 -13.489 13.032 1 11 ? O1B GNP 202 A 1 
HETATM 8 O O2B GNP . . . D 4 -9.801 -13.244 15.345 1 10.23 ? O2B GNP 202 A 1 
HETATM 9 O O3A GNP . . . D 4 -8.555 -12.368 13.302 1 11.88 ? O3A GNP 202 A 1 
HETATM 10 P PA GNP . . . D 4 -7.598 -11.406 14.106 1 11.58 ? PA GNP 202 A 1 
HETATM 11 O O1A GNP . . . D 4 -8.458 -10.344 14.76 1 12.73 ? O1A GNP 202 A 1 
HETATM 12 O O2A GNP . . . D 4 -6.622 -12.228 14.897 1 13.02 ? O2A GNP 202 A 1 
HETATM 13 O O5' GNP . . . D 4 -6.859 -10.695 12.896 1 11.64 ? O5' GNP 202 A 1 
HETATM 14 C C5' GNP . . . D 4 -6.093 -11.458 11.942 1 12.6 ? C5' GNP 202 A 1 
HETATM 15 C C4' GNP . . . D 4 -5.098 -10.524 11.3 1 13.75 ? C4' GNP 202 A 1 
HETATM 16 O O4' GNP . . . D 4 -5.801 -9.525 10.523 1 12.63 ? O4' GNP 202 A 1 
HETATM 17 C C3' GNP . . . D 4 -4.193 -9.753 12.26 1 13.33 ? C3' GNP 202 A 1 
HETATM 18 O O3' GNP . . . D 4 -2.894 -9.607 11.698 1 13.89 ? O3' GNP 202 A 1 
HETATM 19 C C2' GNP . . . D 4 -4.88 -8.391 12.36 1 14.05 ? C2' GNP 202 A 1 
HETATM 20 O O2' GNP . . . D 4 -3.983 -7.327 12.651 1 14.81 ? O2' GNP 202 A 1 
HETATM 21 C C1' GNP . . . D 4 -5.425 -8.231 10.943 1 11.6 ? C1' GNP 202 A 1 
HETATM 22 N N9 GNP . . . D 4 -6.617 -7.381 10.904 1 12.37 ? N9 GNP 202 A 1 
HETATM 23 C C8 GNP . . . D 4 -7.779 -7.56 11.618 1 11.23 ? C8 GNP 202 A 1 
HETATM 24 N N7 GNP . . . D 4 -8.676 -6.636 11.37 1 11.41 ? N7 GNP 202 A 1 
HETATM 25 C C5 GNP . . . D 4 -8.079 -5.823 10.419 1 11.46 ? C5 GNP 202 A 1 
HETATM 26 C C6 GNP . . . D 4 -8.556 -4.626 9.769 1 11.22 ? C6 GNP 202 A 1 
HETATM 27 O O6 GNP . . . D 4 -9.668 -4.111 9.9 1 12.15 ? O6 GNP 202 A 1 
HETATM 28 N N1 GNP . . . D 4 -7.622 -4.109 8.886 1 11.31 ? N1 GNP 202 A 1 
HETATM 29 C C2 GNP . . . D 4 -6.373 -4.629 8.675 1 12.04 ? C2 GNP 202 A 1 
HETATM 30 N N2 GNP . . . D 4 -5.602 -3.999 7.784 1 15.24 ? N2 GNP 202 A 1 
HETATM 31 N N3 GNP . . . D 4 -5.921 -5.729 9.274 1 12.47 ? N3 GNP 202 A 1 
HETATM 32 C C4 GNP . . . D 4 -6.81 -6.26 10.133 1 11.96 ? C4 GNP 202 A 1 
#
_model_server_stats.io_time_ms              27 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    25 
_model_server_stats.query_time_ms           453 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           32 
#