data_5KQ8
#
_model_server_result.job_id            j3_NDx1S5rzMrXdbTAZxWA 
_model_server_result.datetime_utc      '2024-10-11 13:27:16' 
_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          5kq8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":401}' 
#
_entry.id    5KQ8 
#
_exptl.entry_id    5KQ8 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              426.216 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'AMP PHOSPHORAMIDATE' 
_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            5KQ8 
_cell.length_a            98.477 
_cell.length_b            98.477 
_cell.length_c            68.495 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5KQ8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    ? 
_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 
_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' 6_554 -x,-x+y,-z-2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 -45.663333 
#
_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 B O2B AN2 . A AN2 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? 
metalc ? metalc2 C MG MG . A MG 402 1_555 E O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? 
metalc ? metalc3 C MG MG . A MG 402 1_555 E O HOH . A HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? 
metalc ? metalc4 C MG MG . A MG 402 1_555 E O HOH . A HOH 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? 
metalc ? metalc5 C MG MG . A MG 402 1_555 E O HOH . A HOH 527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? 
metalc ? metalc6 C MG MG . A MG 402 1_555 E O HOH . A HOH 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? 
#
_chem_comp.formula           'C10 H16 N6 O9 P2' 
_chem_comp.formula_weight    426.216 
_chem_comp.id                AN2 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'AMP PHOSPHORAMIDATE' 
_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
N3B PB AN2 sing 13 n n 
N3B H3B1 AN2 sing 14 n n 
N3B H3B2 AN2 sing 15 n n 
PB O2B AN2 sing 16 n n 
PB O1B AN2 doub 17 n n 
PB O3A AN2 sing 18 n n 
O2B HO2B AN2 sing 19 n n 
O3A PA AN2 sing 20 n n 
PA O1A AN2 doub 21 n n 
PA O2A AN2 sing 22 n n 
PA O5' AN2 sing 23 n n 
O2A HO2A AN2 sing 24 n n 
O5' C5' AN2 sing 25 n n 
C5' C4' AN2 sing 26 n n 
C5' "H5'1" AN2 sing 27 n n 
C5' "H5'2" AN2 sing 28 n n 
C4' O4' AN2 sing 29 n n 
C4' C3' AN2 sing 30 n n 
C4' H4' AN2 sing 31 n n 
O4' C1' AN2 sing 32 n n 
C3' O3' AN2 sing 33 n n 
C3' C2' AN2 sing 34 n n 
C3' H3' AN2 sing 35 n n 
O3' HA AN2 sing 36 n n 
C2' O2' AN2 sing 37 n n 
C2' C1' AN2 sing 38 n n 
C2' H2' AN2 sing 39 n n 
O2' HB AN2 sing 40 n n 
C1' N9 AN2 sing 41 n n 
C1' H1' AN2 sing 42 n n 
N9 C8 AN2 sing 43 n y 
N9 C4 AN2 sing 44 n y 
C8 N7 AN2 doub 45 n y 
C8 H8 AN2 sing 46 n n 
N7 C5 AN2 sing 47 n y 
C5 C4 AN2 doub 48 n y 
C5 C6 AN2 sing 49 n y 
C4 N3 AN2 sing 50 n y 
N3 C2 AN2 doub 51 n y 
C2 N1 AN2 sing 52 n y 
C2 H2 AN2 sing 53 n n 
N1 C6 AN2 doub 54 n y 
C6 N6 AN2 sing 55 n n 
N6 H6N1 AN2 sing 56 n n 
N6 H6N2 AN2 sing 57 n n 
#
_atom_sites.entry_id                     5KQ8 
_atom_sites.fract_transf_matrix[1][1]    0.010155 
_atom_sites.fract_transf_matrix[1][2]    0.005863 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011726 
_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]    0.0146 
_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 AN2 A 1 401 1 AN2 AN2 . 
C 3 MG A 1 402 1 MG MG . 
D 4 EDO A 1 403 1 EDO EDO . 
E 5 HOH A 1 501 90 HOH HOH . 
E 5 HOH A 2 502 6 HOH HOH . 
E 5 HOH A 3 503 38 HOH HOH . 
E 5 HOH A 4 504 33 HOH HOH . 
E 5 HOH A 5 505 19 HOH HOH . 
E 5 HOH A 6 506 18 HOH HOH . 
E 5 HOH A 7 507 36 HOH HOH . 
E 5 HOH A 8 508 45 HOH HOH . 
E 5 HOH A 9 509 30 HOH HOH . 
E 5 HOH A 10 510 96 HOH HOH . 
E 5 HOH A 11 511 5 HOH HOH . 
E 5 HOH A 12 512 64 HOH HOH . 
E 5 HOH A 13 513 15 HOH HOH . 
E 5 HOH A 14 514 24 HOH HOH . 
E 5 HOH A 15 515 22 HOH HOH . 
E 5 HOH A 16 516 67 HOH HOH . 
E 5 HOH A 17 517 23 HOH HOH . 
E 5 HOH A 18 518 60 HOH HOH . 
E 5 HOH A 19 519 66 HOH HOH . 
E 5 HOH A 20 520 20 HOH HOH . 
E 5 HOH A 21 521 40 HOH HOH . 
E 5 HOH A 22 522 13 HOH HOH . 
E 5 HOH A 23 523 72 HOH HOH . 
E 5 HOH A 24 524 78 HOH HOH . 
E 5 HOH A 25 525 3 HOH HOH . 
E 5 HOH A 26 526 39 HOH HOH . 
E 5 HOH A 27 527 7 HOH HOH . 
E 5 HOH A 28 528 4 HOH HOH . 
E 5 HOH A 29 529 35 HOH HOH . 
E 5 HOH A 30 530 44 HOH HOH . 
E 5 HOH A 31 531 17 HOH HOH . 
E 5 HOH A 32 532 77 HOH HOH . 
E 5 HOH A 33 533 31 HOH HOH . 
E 5 HOH A 34 534 58 HOH HOH . 
E 5 HOH A 35 535 74 HOH HOH . 
E 5 HOH A 36 536 8 HOH HOH . 
E 5 HOH A 37 537 42 HOH HOH . 
E 5 HOH A 38 538 59 HOH HOH . 
E 5 HOH A 39 539 49 HOH HOH . 
E 5 HOH A 40 540 2 HOH HOH . 
E 5 HOH A 41 541 86 HOH HOH . 
E 5 HOH A 42 542 94 HOH HOH . 
E 5 HOH A 43 543 95 HOH HOH . 
E 5 HOH A 44 544 16 HOH HOH . 
E 5 HOH A 45 545 21 HOH HOH . 
E 5 HOH A 46 546 34 HOH HOH . 
E 5 HOH A 47 547 61 HOH HOH . 
E 5 HOH A 48 548 62 HOH HOH . 
E 5 HOH A 49 549 55 HOH HOH . 
E 5 HOH A 50 550 47 HOH HOH . 
E 5 HOH A 51 551 84 HOH HOH . 
E 5 HOH A 52 552 9 HOH HOH . 
E 5 HOH A 53 553 85 HOH HOH . 
E 5 HOH A 54 554 97 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 N N3B AN2 . . . B 2 25.557 -16.784 -12.376 1 30.3 ? N3B AN2 401 A 1 
HETATM 2 P PB AN2 . . . B 2 25.395 -16.55 -10.774 1 32.41 ? PB AN2 401 A 1 
HETATM 3 O O2B AN2 . . . B 2 26.54 -17.103 -10.119 1 35.76 ? O2B AN2 401 A 1 
HETATM 4 O O1B AN2 . . . B 2 25.199 -15.113 -10.398 1 30.33 ? O1B AN2 401 A 1 
HETATM 5 O O3A AN2 . . . B 2 24.094 -17.335 -10.379 1 31.52 ? O3A AN2 401 A 1 
HETATM 6 P PA AN2 . . . B 2 23.508 -17.703 -8.922 1 32.49 ? PA AN2 401 A 1 
HETATM 7 O O1A AN2 . . . B 2 23.78 -19.104 -8.587 1 33.56 ? O1A AN2 401 A 1 
HETATM 8 O O2A AN2 . . . B 2 24.003 -16.745 -7.803 1 31.44 ? O2A AN2 401 A 1 
HETATM 9 O O5' AN2 . . . B 2 21.937 -17.639 -9.193 1 31.16 ? O5' AN2 401 A 1 
HETATM 10 C C5' AN2 . . . B 2 21.411 -16.514 -9.868 1 31.16 ? C5' AN2 401 A 1 
HETATM 11 C C4' AN2 . . . B 2 19.932 -16.816 -10.018 1 34.59 ? C4' AN2 401 A 1 
HETATM 12 O O4' AN2 . . . B 2 19.43 -16.958 -8.78 1 33.01 ? O4' AN2 401 A 1 
HETATM 13 C C3' AN2 . . . B 2 19.167 -15.693 -10.665 1 31.59 ? C3' AN2 401 A 1 
HETATM 14 O O3' AN2 . . . B 2 19.042 -15.884 -11.976 1 34.99 ? O3' AN2 401 A 1 
HETATM 15 C C2' AN2 . . . B 2 17.752 -15.824 -9.983 1 34.4 ? C2' AN2 401 A 1 
HETATM 16 O O2' AN2 . . . B 2 16.954 -16.738 -10.807 1 32.19 ? O2' AN2 401 A 1 
HETATM 17 C C1' AN2 . . . B 2 17.952 -16.35 -8.803 1 34.52 ? C1' AN2 401 A 1 
HETATM 18 N N9 AN2 . . . B 2 17.903 -15.447 -7.666 1 32.33 ? N9 AN2 401 A 1 
HETATM 19 C C8 AN2 . . . B 2 17.623 -15.813 -6.384 1 32.72 ? C8 AN2 401 A 1 
HETATM 20 N N7 AN2 . . . B 2 17.681 -14.707 -5.585 1 36.32 ? N7 AN2 401 A 1 
HETATM 21 C C5 AN2 . . . B 2 17.998 -13.655 -6.371 1 37.46 ? C5 AN2 401 A 1 
HETATM 22 C C4 AN2 . . . B 2 18.147 -14.094 -7.665 1 30.81 ? C4 AN2 401 A 1 
HETATM 23 N N3 AN2 . . . B 2 18.48 -13.186 -8.637 1 32.35 ? N3 AN2 401 A 1 
HETATM 24 C C2 AN2 . . . B 2 18.662 -11.861 -8.32 1 37.42 ? C2 AN2 401 A 1 
HETATM 25 N N1 AN2 . . . B 2 18.506 -11.438 -7.002 1 36.22 ? N1 AN2 401 A 1 
HETATM 26 C C6 AN2 . . . B 2 18.189 -12.314 -6.049 1 38.15 ? C6 AN2 401 A 1 
HETATM 27 N N6 AN2 . . . B 2 18.089 -11.648 -4.777 1 41.33 ? N6 AN2 401 A 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           307 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           27 
#