data_6YX5
#
_model_server_result.job_id            yiYrnFUvI10q07WLYG_CQQ 
_model_server_result.datetime_utc      '2024-12-01 10:22:10' 
_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          6yx5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":202}' 
#
_entry.id    6YX5 
#
_exptl.entry_id    6YX5 
_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         120 
_cell.entry_id            6YX5 
_cell.length_a            142.309 
_cell.length_b            142.309 
_cell.length_c            76.616 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YX5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        150 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 3 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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,F,G,H,I,J,K,L,M,N,O 
_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
covale ? covale1 A OH TYR 75 A TYR 77 1_555 F P14 LJN . A LJN 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.477 ? 
covale ? covale2 F C56 LJN . A LJN 204 1_555 B SG CYS 185 B CYS 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.619 ? 
metalc ? metalc1 A OG1 THR 20 A THR 22 1_555 C MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
metalc ? metalc2 A OG1 THR 38 A THR 40 1_555 C MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? 
metalc ? metalc3 C MG MG . A MG 201 1_555 D O2B GNP . A GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? 
metalc ? metalc4 C MG MG . A MG 201 1_555 D O2G GNP . A GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? 
metalc ? metalc5 C MG MG . A MG 201 1_555 N O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? 
metalc ? metalc6 C MG MG . A MG 201 1_555 N O HOH . A HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
#
_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 153 n n 
PG O2G GNP sing 154 n n 
PG O3G GNP sing 155 n n 
PG N3B GNP sing 156 n n 
O2G HOG2 GNP sing 157 n n 
O3G HOG3 GNP sing 158 n n 
N3B PB GNP sing 159 n n 
N3B HNB3 GNP sing 160 n n 
PB O1B GNP doub 161 n n 
PB O2B GNP sing 162 n n 
PB O3A GNP sing 163 n n 
O2B HOB2 GNP sing 164 n n 
O3A PA GNP sing 165 n n 
PA O1A GNP doub 166 n n 
PA O2A GNP sing 167 n n 
PA O5' GNP sing 168 n n 
O2A HOA2 GNP sing 169 n n 
O5' C5' GNP sing 170 n n 
C5' C4' GNP sing 171 n n 
C5' "H5'2" GNP sing 172 n n 
C5' "H5'1" GNP sing 173 n n 
C4' O4' GNP sing 174 n n 
C4' C3' GNP sing 175 n n 
C4' H4' GNP sing 176 n n 
O4' C1' GNP sing 177 n n 
C3' O3' GNP sing 178 n n 
C3' C2' GNP sing 179 n n 
C3' H3' GNP sing 180 n n 
O3' HO3' GNP sing 181 n n 
C2' O2' GNP sing 182 n n 
C2' C1' GNP sing 183 n n 
C2' H2' GNP sing 184 n n 
O2' HO2' GNP sing 185 n n 
C1' N9 GNP sing 186 n n 
C1' H1' GNP sing 187 n n 
N9 C8 GNP sing 188 n y 
N9 C4 GNP sing 189 n y 
C8 N7 GNP doub 190 n y 
C8 H8 GNP sing 191 n n 
N7 C5 GNP sing 192 n y 
C5 C6 GNP sing 193 n y 
C5 C4 GNP doub 194 n y 
C6 O6 GNP doub 195 n n 
C6 N1 GNP sing 196 n y 
N1 C2 GNP sing 197 n y 
N1 HN1 GNP sing 198 n n 
C2 N2 GNP sing 199 n n 
C2 N3 GNP doub 200 n y 
N2 HN21 GNP sing 201 n n 
N2 HN22 GNP sing 202 n n 
N3 C4 GNP sing 203 n y 
#
_atom_sites.entry_id                     6YX5 
_atom_sites.fract_transf_matrix[1][1]    0.007027 
_atom_sites.fract_transf_matrix[1][2]    0.004057 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008114 
_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]    0.013052 
_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 1 201 202 MG MG . 
D 4 GNP A 1 202 203 GNP GNP . 
E 5 GLC A 1 203 303 GLC GLC . 
F 6 LJN A 1 204 400 LJN LIG . 
G 7 SO4 A 1 205 2 SO4 SO4 . 
H 7 SO4 A 1 206 9 SO4 SO4 . 
I 5 GLC B 1 401 500 GLC GLC . 
J 5 GLC B 1 402 600 GLC GLC . 
K 7 SO4 B 1 403 5 SO4 SO4 . 
L 7 SO4 B 1 404 6 SO4 SO4 . 
M 7 SO4 B 1 405 8 SO4 SO4 . 
N 8 HOH A 1 301 23 HOH HOH . 
N 8 HOH A 2 302 33 HOH HOH . 
N 8 HOH A 3 303 61 HOH HOH . 
N 8 HOH A 4 304 1 HOH HOH . 
N 8 HOH A 5 305 84 HOH HOH . 
N 8 HOH A 6 306 12 HOH HOH . 
N 8 HOH A 7 307 101 HOH HOH . 
N 8 HOH A 8 308 26 HOH HOH . 
N 8 HOH A 9 309 83 HOH HOH . 
N 8 HOH A 10 310 119 HOH HOH . 
N 8 HOH A 11 311 52 HOH HOH . 
N 8 HOH A 12 312 80 HOH HOH . 
N 8 HOH A 13 313 25 HOH HOH . 
N 8 HOH A 14 314 48 HOH HOH . 
N 8 HOH A 15 315 70 HOH HOH . 
N 8 HOH A 16 316 92 HOH HOH . 
N 8 HOH A 17 317 37 HOH HOH . 
N 8 HOH A 18 318 55 HOH HOH . 
N 8 HOH A 19 319 102 HOH HOH . 
N 8 HOH A 20 320 17 HOH HOH . 
N 8 HOH A 21 321 104 HOH HOH . 
N 8 HOH A 22 322 59 HOH HOH . 
N 8 HOH A 23 323 3 HOH HOH . 
N 8 HOH A 24 324 103 HOH HOH . 
N 8 HOH A 25 325 116 HOH HOH . 
N 8 HOH A 26 326 117 HOH HOH . 
N 8 HOH A 27 327 73 HOH HOH . 
O 8 HOH B 1 501 72 HOH HOH . 
O 8 HOH B 2 502 11 HOH HOH . 
O 8 HOH B 3 503 98 HOH HOH . 
O 8 HOH B 4 504 121 HOH HOH . 
O 8 HOH B 5 505 53 HOH HOH . 
O 8 HOH B 6 506 40 HOH HOH . 
O 8 HOH B 7 507 15 HOH HOH . 
O 8 HOH B 8 508 4 HOH HOH . 
O 8 HOH B 9 509 49 HOH HOH . 
O 8 HOH B 10 510 2 HOH HOH . 
O 8 HOH B 11 511 66 HOH HOH . 
O 8 HOH B 12 512 20 HOH HOH . 
O 8 HOH B 13 513 6 HOH HOH . 
O 8 HOH B 14 514 107 HOH HOH . 
O 8 HOH B 15 515 93 HOH HOH . 
O 8 HOH B 16 516 60 HOH HOH . 
O 8 HOH B 17 517 111 HOH HOH . 
O 8 HOH B 18 518 38 HOH HOH . 
O 8 HOH B 19 519 13 HOH HOH . 
O 8 HOH B 20 520 94 HOH HOH . 
O 8 HOH B 21 521 27 HOH HOH . 
O 8 HOH B 22 522 75 HOH HOH . 
O 8 HOH B 23 523 118 HOH HOH . 
O 8 HOH B 24 524 67 HOH HOH . 
O 8 HOH B 25 525 16 HOH HOH . 
O 8 HOH B 26 526 96 HOH HOH . 
O 8 HOH B 27 527 30 HOH HOH . 
O 8 HOH B 28 528 10 HOH HOH . 
O 8 HOH B 29 529 63 HOH HOH . 
O 8 HOH B 30 530 22 HOH HOH . 
O 8 HOH B 31 531 122 HOH HOH . 
O 8 HOH B 32 532 62 HOH HOH . 
O 8 HOH B 33 533 31 HOH HOH . 
O 8 HOH B 34 534 54 HOH HOH . 
O 8 HOH B 35 535 90 HOH HOH . 
O 8 HOH B 36 536 34 HOH HOH . 
O 8 HOH B 37 537 28 HOH HOH . 
O 8 HOH B 38 538 9 HOH HOH . 
O 8 HOH B 39 539 8 HOH HOH . 
O 8 HOH B 40 540 42 HOH HOH . 
O 8 HOH B 41 541 65 HOH HOH . 
O 8 HOH B 42 542 43 HOH HOH . 
O 8 HOH B 43 543 24 HOH HOH . 
O 8 HOH B 44 544 18 HOH HOH . 
O 8 HOH B 45 545 35 HOH HOH . 
O 8 HOH B 46 546 39 HOH HOH . 
O 8 HOH B 47 547 36 HOH HOH . 
O 8 HOH B 48 548 82 HOH HOH . 
O 8 HOH B 49 549 19 HOH HOH . 
O 8 HOH B 50 550 14 HOH HOH . 
O 8 HOH B 51 551 46 HOH HOH . 
O 8 HOH B 52 552 68 HOH HOH . 
O 8 HOH B 53 553 89 HOH HOH . 
O 8 HOH B 54 554 99 HOH HOH . 
O 8 HOH B 55 555 21 HOH HOH . 
O 8 HOH B 56 556 85 HOH HOH . 
O 8 HOH B 57 557 112 HOH HOH . 
O 8 HOH B 58 558 57 HOH HOH . 
O 8 HOH B 59 559 110 HOH HOH . 
O 8 HOH B 60 560 100 HOH HOH . 
O 8 HOH B 61 561 81 HOH HOH . 
O 8 HOH B 62 562 51 HOH HOH . 
O 8 HOH B 63 563 74 HOH HOH . 
O 8 HOH B 64 564 71 HOH HOH . 
O 8 HOH B 65 565 88 HOH HOH . 
O 8 HOH B 66 566 76 HOH HOH . 
O 8 HOH B 67 567 108 HOH HOH . 
O 8 HOH B 68 568 7 HOH HOH . 
O 8 HOH B 69 569 87 HOH HOH . 
O 8 HOH B 70 570 95 HOH HOH . 
O 8 HOH B 71 571 86 HOH HOH . 
O 8 HOH B 72 572 78 HOH HOH . 
O 8 HOH B 73 573 113 HOH HOH . 
O 8 HOH B 74 574 115 HOH HOH . 
O 8 HOH B 75 575 47 HOH HOH . 
O 8 HOH B 76 576 109 HOH HOH . 
O 8 HOH B 77 577 58 HOH HOH . 
O 8 HOH B 78 578 105 HOH HOH . 
O 8 HOH B 79 579 64 HOH HOH . 
O 8 HOH B 80 580 77 HOH HOH . 
O 8 HOH B 81 581 29 HOH HOH . 
O 8 HOH B 82 582 120 HOH HOH . 
O 8 HOH B 83 583 50 HOH HOH . 
O 8 HOH B 84 584 41 HOH HOH . 
O 8 HOH B 85 585 91 HOH HOH . 
O 8 HOH B 86 586 106 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 -28.124 -66.521 9.034 1 32.43 ? PG GNP 202 A 1 
HETATM 2 O O1G GNP . . . D 4 -29.377 -66.066 9.729 1 30.99 ? O1G GNP 202 A 1 
HETATM 3 O O2G GNP . . . D 4 -26.903 -65.754 9.469 1 28.7 ? O2G GNP 202 A 1 
HETATM 4 O O3G GNP . . . D 4 -28.263 -66.552 7.522 1 30.74 ? O3G GNP 202 A 1 
HETATM 5 N N3B GNP . . . D 4 -27.894 -68.07 9.496 1 32.76 ? N3B GNP 202 A 1 
HETATM 6 P PB GNP . . . D 4 -26.726 -69.103 9.11 1 30.9 ? PB GNP 202 A 1 
HETATM 7 O O1B GNP . . . D 4 -27.05 -69.76 7.809 1 33.18 ? O1B GNP 202 A 1 
HETATM 8 O O2B GNP . . . D 4 -25.439 -68.362 9.262 1 27.63 ? O2B GNP 202 A 1 
HETATM 9 O O3A GNP . . . D 4 -26.828 -70.217 10.253 1 32.72 ? O3A GNP 202 A 1 
HETATM 10 P PA GNP . . . D 4 -25.885 -70.453 11.529 1 32.8 ? PA GNP 202 A 1 
HETATM 11 O O1A GNP . . . D 4 -24.5 -70.767 11.069 1 30.24 ? O1A GNP 202 A 1 
HETATM 12 O O2A GNP . . . D 4 -26.071 -69.288 12.441 1 29.49 ? O2A GNP 202 A 1 
HETATM 13 O O5' GNP . . . D 4 -26.546 -71.77 12.163 1 32.75 ? O5' GNP 202 A 1 
HETATM 14 C C5' GNP . . . D 4 -27.938 -71.753 12.562 1 33.8 ? C5' GNP 202 A 1 
HETATM 15 C C4' GNP . . . D 4 -28.188 -72.857 13.56 1 33.86 ? C4' GNP 202 A 1 
HETATM 16 O O4' GNP . . . D 4 -27.884 -74.137 12.948 1 36.79 ? O4' GNP 202 A 1 
HETATM 17 C C3' GNP . . . D 4 -27.352 -72.805 14.846 1 34.83 ? C3' GNP 202 A 1 
HETATM 18 O O3' GNP . . . D 4 -28.106 -73.253 15.964 1 33.92 ? O3' GNP 202 A 1 
HETATM 19 C C2' GNP . . . D 4 -26.205 -73.771 14.547 1 37.19 ? C2' GNP 202 A 1 
HETATM 20 O O2' GNP . . . D 4 -25.635 -74.336 15.709 1 36.63 ? O2' GNP 202 A 1 
HETATM 21 C C1' GNP . . . D 4 -26.922 -74.828 13.714 1 35.42 ? C1' GNP 202 A 1 
HETATM 22 N N9 GNP . . . D 4 -26.028 -75.554 12.819 1 32.25 ? N9 GNP 202 A 1 
HETATM 23 C C8 GNP . . . D 4 -25.184 -75.015 11.88 1 31.99 ? C8 GNP 202 A 1 
HETATM 24 N N7 GNP . . . D 4 -24.481 -75.913 11.233 1 32.71 ? N7 GNP 202 A 1 
HETATM 25 C C5 GNP . . . D 4 -24.885 -77.122 11.784 1 32.64 ? C5 GNP 202 A 1 
HETATM 26 C C6 GNP . . . D 4 -24.474 -78.447 11.485 1 35.12 ? C6 GNP 202 A 1 
HETATM 27 O O6 GNP . . . D 4 -23.639 -78.826 10.651 1 36.01 ? O6 GNP 202 A 1 
HETATM 28 N N1 GNP . . . D 4 -25.141 -79.379 12.281 1 33.94 ? N1 GNP 202 A 1 
HETATM 29 C C2 GNP . . . D 4 -26.085 -79.084 13.233 1 34.37 ? C2 GNP 202 A 1 
HETATM 30 N N2 GNP . . . D 4 -26.622 -80.121 13.89 1 36.65 ? N2 GNP 202 A 1 
HETATM 31 N N3 GNP . . . D 4 -26.473 -77.842 13.521 1 34.75 ? N3 GNP 202 A 1 
HETATM 32 C C4 GNP . . . D 4 -25.837 -76.916 12.76 1 34.04 ? C4 GNP 202 A 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           238 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           32 
#