data_6X4L
#
_model_server_result.job_id            yd9x5XTKMLLcY_sC0pE48g 
_model_server_result.datetime_utc      '2025-07-07 08:36:54' 
_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          6x4l 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":402}' 
#
_entry.id    6X4L 
#
_exptl.entry_id    6X4L 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              506.196 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE 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            6X4L 
_cell.length_a            98.514 
_cell.length_b            98.514 
_cell.length_c            68.82 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6X4L 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    'P 31 2"' 
_symmetry.space_group_name_H-M     'P 31 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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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' 5_554 x-y,-y,-z-1/3 1 0 0 0 -1 0 0 0 -1 0 0 -22.94 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_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 C O3G ANP . A ANP 402 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.917 ? 
metalc ? metalc2 C O1B ANP . A ANP 402 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? 
metalc ? metalc3 D MG MG . A MG 403 1_555 H O HOH . A HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? 
metalc ? metalc4 D MG MG . A MG 403 1_555 H O HOH . A HOH 529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? 
metalc ? metalc5 D MG MG . A MG 403 1_555 H O HOH . A HOH 530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? 
metalc ? metalc6 D MG MG . A MG 403 1_555 H O HOH . A HOH 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? 
#
_chem_comp.formula           'C10 H17 N6 O12 P3' 
_chem_comp.formula_weight    506.196 
_chem_comp.id                ANP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE 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 ANP doub 13 n n 
PG O2G ANP sing 14 n n 
PG O3G ANP sing 15 n n 
PG N3B ANP sing 16 n n 
O2G HOG2 ANP sing 17 n n 
O3G HOG3 ANP sing 18 n n 
PB O1B ANP doub 19 n n 
PB O2B ANP sing 20 n n 
PB N3B ANP sing 21 n n 
PB O3A ANP sing 22 n n 
O2B HOB2 ANP sing 23 n n 
N3B HNB1 ANP sing 24 n n 
PA O1A ANP doub 25 n n 
PA O2A ANP sing 26 n n 
PA O3A ANP sing 27 n n 
PA O5' ANP sing 28 n n 
O2A HOA2 ANP sing 29 n n 
O5' C5' ANP sing 30 n n 
C5' C4' ANP sing 31 n n 
C5' "H5'1" ANP sing 32 n n 
C5' "H5'2" ANP sing 33 n n 
C4' O4' ANP sing 34 n n 
C4' C3' ANP sing 35 n n 
C4' H4' ANP sing 36 n n 
O4' C1' ANP sing 37 n n 
C3' O3' ANP sing 38 n n 
C3' C2' ANP sing 39 n n 
C3' H3' ANP sing 40 n n 
O3' HO3' ANP sing 41 n n 
C2' O2' ANP sing 42 n n 
C2' C1' ANP sing 43 n n 
C2' H2' ANP sing 44 n n 
O2' HO2' ANP sing 45 n n 
C1' N9 ANP sing 46 n n 
C1' H1' ANP sing 47 n n 
N9 C8 ANP sing 48 n y 
N9 C4 ANP sing 49 n y 
C8 N7 ANP doub 50 n y 
C8 H8 ANP sing 51 n n 
N7 C5 ANP sing 52 n y 
C5 C6 ANP sing 53 n y 
C5 C4 ANP doub 54 n y 
C6 N6 ANP sing 55 n n 
C6 N1 ANP doub 56 n y 
N6 HN61 ANP sing 57 n n 
N6 HN62 ANP sing 58 n n 
N1 C2 ANP sing 59 n y 
C2 N3 ANP doub 60 n y 
C2 H2 ANP sing 61 n n 
N3 C4 ANP sing 62 n y 
#
_atom_sites.entry_id                     6X4L 
_atom_sites.fract_transf_matrix[1][1]    0.010151 
_atom_sites.fract_transf_matrix[1][2]    0.005861 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011721 
_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]    0.014531 
_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 UOS A 1 401 1 UOS Y86 . 
C 3 ANP A 1 402 501 ANP ANP . 
D 4 MG A 1 403 1 MG MG . 
E 5 EDO A 1 404 1 EDO EDO . 
F 5 EDO A 1 405 2 EDO EDO . 
G 6 CL A 1 406 1 CL CL . 
H 7 HOH A 1 501 182 HOH HOH . 
H 7 HOH A 2 502 19 HOH HOH . 
H 7 HOH A 3 503 220 HOH HOH . 
H 7 HOH A 4 504 57 HOH HOH . 
H 7 HOH A 5 505 113 HOH HOH . 
H 7 HOH A 6 506 8 HOH HOH . 
H 7 HOH A 7 507 46 HOH HOH . 
H 7 HOH A 8 508 54 HOH HOH . 
H 7 HOH A 9 509 5 HOH HOH . 
H 7 HOH A 10 510 70 HOH HOH . 
H 7 HOH A 11 511 62 HOH HOH . 
H 7 HOH A 12 512 20 HOH HOH . 
H 7 HOH A 13 513 10 HOH HOH . 
H 7 HOH A 14 514 78 HOH HOH . 
H 7 HOH A 15 515 59 HOH HOH . 
H 7 HOH A 16 516 29 HOH HOH . 
H 7 HOH A 17 517 235 HOH HOH . 
H 7 HOH A 18 518 40 HOH HOH . 
H 7 HOH A 19 519 55 HOH HOH . 
H 7 HOH A 20 520 204 HOH HOH . 
H 7 HOH A 21 521 51 HOH HOH . 
H 7 HOH A 22 522 2 HOH HOH . 
H 7 HOH A 23 523 192 HOH HOH . 
H 7 HOH A 24 524 36 HOH HOH . 
H 7 HOH A 25 525 227 HOH HOH . 
H 7 HOH A 26 526 50 HOH HOH . 
H 7 HOH A 27 527 193 HOH HOH . 
H 7 HOH A 28 528 26 HOH HOH . 
H 7 HOH A 29 529 7 HOH HOH . 
H 7 HOH A 30 530 6 HOH HOH . 
H 7 HOH A 31 531 152 HOH HOH . 
H 7 HOH A 32 532 228 HOH HOH . 
H 7 HOH A 33 533 21 HOH HOH . 
H 7 HOH A 34 534 211 HOH HOH . 
H 7 HOH A 35 535 225 HOH HOH . 
H 7 HOH A 36 536 203 HOH HOH . 
H 7 HOH A 37 537 11 HOH HOH . 
H 7 HOH A 38 538 47 HOH HOH . 
H 7 HOH A 39 539 48 HOH HOH . 
H 7 HOH A 40 540 226 HOH HOH . 
H 7 HOH A 41 541 200 HOH HOH . 
H 7 HOH A 42 542 27 HOH HOH . 
H 7 HOH A 43 543 221 HOH HOH . 
H 7 HOH A 44 544 23 HOH HOH . 
H 7 HOH A 45 545 34 HOH HOH . 
H 7 HOH A 46 546 4 HOH HOH . 
H 7 HOH A 47 547 18 HOH HOH . 
H 7 HOH A 48 548 194 HOH HOH . 
H 7 HOH A 49 549 66 HOH HOH . 
H 7 HOH A 50 550 93 HOH HOH . 
H 7 HOH A 51 551 199 HOH HOH . 
H 7 HOH A 52 552 60 HOH HOH . 
H 7 HOH A 53 553 42 HOH HOH . 
H 7 HOH A 54 554 56 HOH HOH . 
H 7 HOH A 55 555 189 HOH HOH . 
H 7 HOH A 56 556 38 HOH HOH . 
H 7 HOH A 57 557 195 HOH HOH . 
H 7 HOH A 58 558 236 HOH HOH . 
H 7 HOH A 59 559 230 HOH HOH . 
H 7 HOH A 60 560 179 HOH HOH . 
H 7 HOH A 61 561 37 HOH HOH . 
H 7 HOH A 62 562 65 HOH HOH . 
H 7 HOH A 63 563 188 HOH HOH . 
H 7 HOH A 64 564 153 HOH HOH . 
H 7 HOH A 65 565 206 HOH HOH . 
H 7 HOH A 66 566 234 HOH HOH . 
H 7 HOH A 67 567 76 HOH HOH . 
H 7 HOH A 68 568 16 HOH HOH . 
H 7 HOH A 69 569 35 HOH HOH . 
H 7 HOH A 70 570 210 HOH HOH . 
H 7 HOH A 71 571 162 HOH HOH . 
H 7 HOH A 72 572 49 HOH HOH . 
H 7 HOH A 73 573 184 HOH HOH . 
H 7 HOH A 74 574 33 HOH HOH . 
H 7 HOH A 75 575 82 HOH HOH . 
H 7 HOH A 76 576 214 HOH HOH . 
H 7 HOH A 77 577 61 HOH HOH . 
H 7 HOH A 78 578 202 HOH HOH . 
H 7 HOH A 79 579 198 HOH HOH . 
H 7 HOH A 80 580 218 HOH HOH . 
H 7 HOH A 81 581 161 HOH HOH . 
H 7 HOH A 82 582 219 HOH HOH . 
H 7 HOH A 83 583 213 HOH HOH . 
H 7 HOH A 84 584 197 HOH HOH . 
H 7 HOH A 85 585 216 HOH HOH . 
H 7 HOH A 86 586 208 HOH HOH . 
H 7 HOH A 87 587 103 HOH HOH . 
H 7 HOH A 88 588 231 HOH HOH . 
H 7 HOH A 89 589 127 HOH HOH . 
H 7 HOH A 90 590 205 HOH HOH . 
H 7 HOH A 91 591 196 HOH HOH . 
H 7 HOH A 92 592 209 HOH HOH . 
H 7 HOH A 93 593 237 HOH HOH . 
H 7 HOH A 94 594 215 HOH HOH . 
H 7 HOH A 95 595 122 HOH HOH . 
H 7 HOH A 96 596 233 HOH HOH . 
H 7 HOH A 97 597 156 HOH HOH . 
H 7 HOH A 98 598 217 HOH HOH . 
H 7 HOH A 99 599 58 HOH HOH . 
H 7 HOH A 100 600 207 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 ANP . . . C 3 -28.538 -14.212 -1.719 1 39.73 ? PG ANP 402 A 1 
HETATM 2 O O1G ANP . . . C 3 -28.788 -13.285 -2.916 1 39.04 ? O1G ANP 402 A 1 
HETATM 3 O O2G ANP . . . C 3 -28.227 -15.64 -2.272 1 34.96 ? O2G ANP 402 A 1 
HETATM 4 O O3G ANP . . . C 3 -29.841 -14.193 -0.83 1 37.1 ? O3G ANP 402 A 1 
HETATM 5 P PB ANP . . . C 3 -26.983 -13.668 0.684 1 29.57 ? PB ANP 402 A 1 
HETATM 6 O O1B ANP . . . C 3 -28.088 -14.428 1.356 1 29.71 ? O1B ANP 402 A 1 
HETATM 7 O O2B ANP . . . C 3 -25.634 -14.304 1.029 1 29.7 ? O2B ANP 402 A 1 
HETATM 8 N N3B ANP . . . C 3 -27.134 -13.649 -0.96 1 28.75 ? N3B ANP 402 A 1 
HETATM 9 P PA ANP . . . C 3 -27.106 -11.488 2.53 1 31.12 ? PA ANP 402 A 1 
HETATM 10 O O1A ANP . . . C 3 -26.464 -12.325 3.58 1 31.4 ? O1A ANP 402 A 1 
HETATM 11 O O2A ANP . . . C 3 -28.534 -11.081 2.867 1 31.14 ? O2A ANP 402 A 1 
HETATM 12 O O3A ANP . . . C 3 -27.011 -12.157 1.083 1 27.21 ? O3A ANP 402 A 1 
HETATM 13 O O5' ANP . . . C 3 -26.257 -10.172 2.267 1 27.46 ? O5' ANP 402 A 1 
HETATM 14 C C5' ANP . . . C 3 -24.999 -10.226 1.573 1 28.54 ? C5' ANP 402 A 1 
HETATM 15 C C4' ANP . . . C 3 -24.469 -8.821 1.404 1 29.79 ? C4' ANP 402 A 1 
HETATM 16 O O4' ANP . . . C 3 -24.273 -8.218 2.696 1 31.21 ? O4' ANP 402 A 1 
HETATM 17 C C3' ANP . . . C 3 -23.129 -8.702 0.685 1 27.84 ? C3' ANP 402 A 1 
HETATM 18 O O3' ANP . . . C 3 -23.37 -8.515 -0.704 1 30.43 ? O3' ANP 402 A 1 
HETATM 19 C C2' ANP . . . C 3 -22.531 -7.418 1.272 1 34.48 ? C2' ANP 402 A 1 
HETATM 20 O O2' ANP . . . C 3 -22.966 -6.261 0.57 1 30.5 ? O2' ANP 402 A 1 
HETATM 21 C C1' ANP . . . C 3 -23.136 -7.373 2.682 1 30.22 ? C1' ANP 402 A 1 
HETATM 22 N N9 ANP . . . C 3 -22.252 -7.793 3.76 1 28.46 ? N9 ANP 402 A 1 
HETATM 23 C C8 ANP . . . C 3 -22.383 -7.404 5.069 1 28.53 ? C8 ANP 402 A 1 
HETATM 24 N N7 ANP . . . C 3 -21.505 -7.941 5.877 1 33.55 ? N7 ANP 402 A 1 
HETATM 25 C C5 ANP . . . C 3 -20.743 -8.749 5.047 1 32.17 ? C5 ANP 402 A 1 
HETATM 26 C C6 ANP . . . C 3 -19.637 -9.58 5.294 1 33.55 ? C6 ANP 402 A 1 
HETATM 27 N N6 ANP . . . C 3 -19.101 -9.752 6.503 1 38.35 ? N6 ANP 402 A 1 
HETATM 28 N N1 ANP . . . C 3 -19.113 -10.256 4.246 1 32.2 ? N1 ANP 402 A 1 
HETATM 29 C C2 ANP . . . C 3 -19.666 -10.102 3.039 1 37.53 ? C2 ANP 402 A 1 
HETATM 30 N N3 ANP . . . C 3 -20.705 -9.339 2.686 1 34.15 ? N3 ANP 402 A 1 
HETATM 31 C C4 ANP . . . C 3 -21.201 -8.68 3.741 1 29.83 ? C4 ANP 402 A 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           25 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           269 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           31 
#