data_6YBB
#
_model_server_result.job_id            rKAk-oG9aVpTA3BAmAHfMw 
_model_server_result.datetime_utc      '2024-11-16 01:51:28' 
_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          6ybb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":302}' 
#
_entry.id    6YBB 
#
_exptl.entry_id    6YBB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              507.181 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_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            6YBB 
_cell.length_a            61.43 
_cell.length_b            169.59 
_cell.length_c            177.6 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YBB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    'P 2ac 2ab' 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,P,Q,R,S,T,U 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 5 H N N 
? 5 J N 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 OG1 THR 16 A THR 16 1_555 G MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
metalc ? metalc2 G MG MG . A MG 301 1_555 H O3G ATP . A ATP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? 
metalc ? metalc3 G MG MG . A MG 301 1_555 H O2B ATP . A ATP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? 
metalc ? metalc4 G MG MG . A MG 301 1_555 H O1A ATP . A ATP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.873 ? 
metalc ? metalc5 G MG MG . A MG 301 1_555 Q O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? 
metalc ? metalc6 G MG MG . A MG 301 1_555 Q O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? 
metalc ? metalc7 B OG1 THR 16 B THR 16 1_555 I MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? 
metalc ? metalc8 I MG MG . B MG 301 1_555 J O2B ATP . B ATP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? 
metalc ? metalc9 I MG MG . B MG 301 1_555 J O3G ATP . B ATP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? 
metalc ? metalc10 I MG MG . B MG 301 1_555 R O HOH . B HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? 
metalc ? metalc11 I MG MG . B MG 301 1_555 R O HOH . B HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.611 ? 
#
_chem_comp.formula           'C10 H16 N5 O13 P3' 
_chem_comp.formula_weight    507.181 
_chem_comp.id                ATP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "ADENOSINE-5'-TRIPHOSPHATE" 
_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 ATP doub 70 n n 
PG O2G ATP sing 71 n n 
PG O3G ATP sing 72 n n 
PG O3B ATP sing 73 n n 
O2G HOG2 ATP sing 74 n n 
O3G HOG3 ATP sing 75 n n 
PB O1B ATP doub 76 n n 
PB O2B ATP sing 77 n n 
PB O3B ATP sing 78 n n 
PB O3A ATP sing 79 n n 
O2B HOB2 ATP sing 80 n n 
PA O1A ATP doub 81 n n 
PA O2A ATP sing 82 n n 
PA O3A ATP sing 83 n n 
PA O5' ATP sing 84 n n 
O2A HOA2 ATP sing 85 n n 
O5' C5' ATP sing 86 n n 
C5' C4' ATP sing 87 n n 
C5' "H5'1" ATP sing 88 n n 
C5' "H5'2" ATP sing 89 n n 
C4' O4' ATP sing 90 n n 
C4' C3' ATP sing 91 n n 
C4' H4' ATP sing 92 n n 
O4' C1' ATP sing 93 n n 
C3' O3' ATP sing 94 n n 
C3' C2' ATP sing 95 n n 
C3' H3' ATP sing 96 n n 
O3' HO3' ATP sing 97 n n 
C2' O2' ATP sing 98 n n 
C2' C1' ATP sing 99 n n 
C2' H2' ATP sing 100 n n 
O2' HO2' ATP sing 101 n n 
C1' N9 ATP sing 102 n n 
C1' H1' ATP sing 103 n n 
N9 C8 ATP sing 104 n y 
N9 C4 ATP sing 105 n y 
C8 N7 ATP doub 106 n y 
C8 H8 ATP sing 107 n n 
N7 C5 ATP sing 108 n y 
C5 C6 ATP sing 109 n y 
C5 C4 ATP doub 110 n y 
C6 N6 ATP sing 111 n n 
C6 N1 ATP doub 112 n y 
N6 HN61 ATP sing 113 n n 
N6 HN62 ATP sing 114 n n 
N1 C2 ATP sing 115 n y 
C2 N3 ATP doub 116 n y 
C2 H2 ATP sing 117 n n 
N3 C4 ATP sing 118 n y 
#
_atom_sites.entry_id                     6YBB 
_atom_sites.fract_transf_matrix[1][1]    0.016279 
_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]    0.005897 
_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]    0.005631 
_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
G 4 MG A 1 301 1 MG MG . 
H 5 ATP A 1 302 1 ATP ATP . 
I 4 MG B 1 301 2 MG MG . 
J 5 ATP B 1 302 2 ATP ATP . 
K 6 C2E E 1 601 3 C2E C2E . 
L 6 C2E E 1 602 4 C2E C2E . 
M 7 GOL E 1 603 1 GOL GOL . 
N 6 C2E F 1 601 1 C2E C2E . 
O 6 C2E F 1 602 2 C2E C2E . 
P 7 GOL F 1 603 2 GOL GOL . 
Q 8 HOH A 1 401 52 HOH HOH . 
Q 8 HOH A 2 402 31 HOH HOH . 
Q 8 HOH A 3 403 41 HOH HOH . 
Q 8 HOH A 4 404 7 HOH HOH . 
Q 8 HOH A 5 405 40 HOH HOH . 
Q 8 HOH A 6 406 2 HOH HOH . 
R 8 HOH B 1 401 11 HOH HOH . 
R 8 HOH B 2 402 9 HOH HOH . 
R 8 HOH B 3 403 23 HOH HOH . 
S 8 HOH D 1 101 19 HOH HOH . 
S 8 HOH D 2 102 26 HOH HOH . 
T 8 HOH E 1 701 66 HOH HOH . 
T 8 HOH E 2 702 56 HOH HOH . 
T 8 HOH E 3 703 6 HOH HOH . 
T 8 HOH E 4 704 4 HOH HOH . 
T 8 HOH E 5 705 16 HOH HOH . 
T 8 HOH E 6 706 5 HOH HOH . 
T 8 HOH E 7 707 47 HOH HOH . 
U 8 HOH F 1 701 51 HOH HOH . 
U 8 HOH F 2 702 65 HOH HOH . 
U 8 HOH F 3 703 60 HOH HOH . 
U 8 HOH F 4 704 27 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 ATP . . . H 5 77.926 182.793 44.671 1 103.59 ? PG ATP 302 A 1 
HETATM 2 O O1G ATP . . . H 5 79.398 182.923 44.84 1 101.21 ? O1G ATP 302 A 1 
HETATM 3 O O2G ATP . . . H 5 77.454 181.336 44.592 1 105.55 ? O2G ATP 302 A 1 
HETATM 4 O O3G ATP . . . H 5 77.114 183.506 45.765 1 114.29 ? O3G ATP 302 A 1 
HETATM 5 P PB ATP . . . H 5 76.554 184.687 42.915 1 100.52 ? PB ATP 302 A 1 
HETATM 6 O O1B ATP . . . H 5 75.222 184.214 42.492 1 123.22 ? O1B ATP 302 A 1 
HETATM 7 O O2B ATP . . . H 5 76.602 185.682 44.082 1 108.53 ? O2B ATP 302 A 1 
HETATM 8 O O3B ATP . . . H 5 77.504 183.467 43.291 1 104.1 ? O3B ATP 302 A 1 
HETATM 9 P PA ATP . . . H 5 78.708 186.169 41.623 1 88.52 ? PA ATP 302 A 1 
HETATM 10 O O1A ATP . . . H 5 79.438 186.057 42.908 1 95.34 ? O1A ATP 302 A 1 
HETATM 11 O O2A ATP . . . H 5 78.354 187.582 41.128 1 81.04 ? O2A ATP 302 A 1 
HETATM 12 O O3A ATP . . . H 5 77.348 185.347 41.705 1 95.05 ? O3A ATP 302 A 1 
HETATM 13 O O5' ATP . . . H 5 79.512 185.443 40.438 1 83.16 ? O5' ATP 302 A 1 
HETATM 14 C C5' ATP . . . H 5 78.996 185.36 39.093 1 79.11 ? C5' ATP 302 A 1 
HETATM 15 C C4' ATP . . . H 5 80.173 185.318 38.153 1 79.3 ? C4' ATP 302 A 1 
HETATM 16 O O4' ATP . . . H 5 79.715 185.524 36.8 1 78.01 ? O4' ATP 302 A 1 
HETATM 17 C C3' ATP . . . H 5 81.195 186.421 38.387 1 82.86 ? C3' ATP 302 A 1 
HETATM 18 O O3' ATP . . . H 5 82.483 186.076 37.885 1 81.62 ? O3' ATP 302 A 1 
HETATM 19 C C2' ATP . . . H 5 80.574 187.586 37.618 1 84.86 ? C2' ATP 302 A 1 
HETATM 20 O O2' ATP . . . H 5 81.548 188.567 37.272 1 85.71 ? O2' ATP 302 A 1 
HETATM 21 C C1' ATP . . . H 5 79.978 186.86 36.401 1 80.41 ? C1' ATP 302 A 1 
HETATM 22 N N9 ATP . . . H 5 78.737 187.445 35.901 1 78.2 ? N9 ATP 302 A 1 
HETATM 23 C C8 ATP . . . H 5 77.583 187.679 36.606 1 76.72 ? C8 ATP 302 A 1 
HETATM 24 N N7 ATP . . . H 5 76.631 188.242 35.902 1 74.19 ? N7 ATP 302 A 1 
HETATM 25 C C5 ATP . . . H 5 77.194 188.386 34.641 1 80.43 ? C5 ATP 302 A 1 
HETATM 26 C C6 ATP . . . H 5 76.696 188.907 33.433 1 86.44 ? C6 ATP 302 A 1 
HETATM 27 N N6 ATP . . . H 5 75.465 189.41 33.288 1 85.88 ? N6 ATP 302 A 1 
HETATM 28 N N1 ATP . . . H 5 77.514 188.889 32.358 1 97.07 ? N1 ATP 302 A 1 
HETATM 29 C C2 ATP . . . H 5 78.742 188.381 32.493 1 105.68 ? C2 ATP 302 A 1 
HETATM 30 N N3 ATP . . . H 5 79.321 187.866 33.58 1 94.61 ? N3 ATP 302 A 1 
HETATM 31 C C4 ATP . . . H 5 78.49 187.896 34.628 1 86.12 ? C4 ATP 302 A 1 
#
_model_server_stats.io_time_ms              31 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           301 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           31 
#