data_6OFB
#
_model_server_result.job_id            1fsyaSL1JzOZnsA3pSXUdA 
_model_server_result.datetime_utc      '2025-08-31 00:24:30' 
_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          6ofb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":902}' 
#
_entry.id    6OFB 
#
_exptl.entry_id    6OFB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              347.221 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'ADENOSINE MONOPHOSPHATE' 
_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            6OFB 
_cell.length_a            102.25 
_cell.length_b            198.89 
_cell.length_c            219.69 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6OFB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    'I 2 2' 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_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    1,2,3,4 
#
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' 2_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 198.89 0 
3 'crystal symmetry operation' 3_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 0 0 219.69 
4 'crystal symmetry operation' 4_566 x,-y+1,-z+1 1 0 0 0 -1 0 0 0 -1 0 198.89 219.69 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 M 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 N VAL 361 A VAL 360 1_555 F MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.714 ? 
metalc ? metalc2 A N ASP 362 A ASP 361 1_555 F MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.768 ? 
metalc ? metalc3 E O2 POP . A POP 903 1_555 F MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.873 ? 
metalc ? metalc4 E O3 POP . A POP 903 1_555 F MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.957 ? 
metalc ? metalc5 E O5 POP . A POP 903 1_555 F MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.742 ? 
metalc ? metalc6 B N VAL 361 B VAL 360 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.908 ? 
metalc ? metalc7 B N ASP 362 B ASP 361 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.843 ? 
metalc ? metalc8 N O1 POP . B POP 903 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.873 ? 
metalc ? metalc9 N O3 POP . B POP 903 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.957 ? 
metalc ? metalc10 N O5 POP . B POP 903 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.741 ? 
#
_chem_comp.formula           'C10 H14 N5 O7 P' 
_chem_comp.formula_weight    347.221 
_chem_comp.id                AMP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'ADENOSINE MONOPHOSPHATE' 
_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
P O1P AMP doub 13 n n 
P O2P AMP sing 14 n n 
P O3P AMP sing 15 n n 
P O5' AMP sing 16 n n 
O2P HOP2 AMP sing 17 n n 
O3P HOP3 AMP sing 18 n n 
O5' C5' AMP sing 19 n n 
C5' C4' AMP sing 20 n n 
C5' "H5'1" AMP sing 21 n n 
C5' "H5'2" AMP sing 22 n n 
C4' O4' AMP sing 23 n n 
C4' C3' AMP sing 24 n n 
C4' H4' AMP sing 25 n n 
O4' C1' AMP sing 26 n n 
C3' O3' AMP sing 27 n n 
C3' C2' AMP sing 28 n n 
C3' H3' AMP sing 29 n n 
O3' HO3' AMP sing 30 n n 
C2' O2' AMP sing 31 n n 
C2' C1' AMP sing 32 n n 
C2' H2' AMP sing 33 n n 
O2' HO2' AMP sing 34 n n 
C1' N9 AMP sing 35 n n 
C1' H1' AMP sing 36 n n 
N9 C8 AMP sing 37 n y 
N9 C4 AMP sing 38 n y 
C8 N7 AMP doub 39 n y 
C8 H8 AMP sing 40 n n 
N7 C5 AMP sing 41 n y 
C5 C6 AMP sing 42 n y 
C5 C4 AMP doub 43 n y 
C6 N6 AMP sing 44 n n 
C6 N1 AMP doub 45 n y 
N6 HN61 AMP sing 46 n n 
N6 HN62 AMP sing 47 n n 
N1 C2 AMP sing 48 n y 
C2 N3 AMP doub 49 n y 
C2 H2 AMP sing 50 n n 
N3 C4 AMP sing 51 n y 
#
_atom_sites.entry_id                     6OFB 
_atom_sites.fract_transf_matrix[1][1]    0.00978 
_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]    0.005028 
_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]    0.004552 
_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 2 DND A 1 901 901 DND NXX . 
D 3 AMP A 1 902 902 AMP AMP . 
E 4 POP A 1 903 903 POP POP . 
F 5 MG A 1 904 904 MG MG . 
G 6 CL A 1 905 905 CL CL . 
H 6 CL A 1 906 906 CL CL . 
I 6 CL A 1 907 907 CL CL . 
J 6 CL A 1 908 908 CL CL . 
K 6 CL A 1 909 909 CL CL . 
L 2 DND B 1 901 901 DND NXX . 
M 3 AMP B 1 902 902 AMP AMP . 
N 4 POP B 1 903 903 POP POP . 
O 5 MG B 1 904 904 MG MG . 
P 6 CL B 1 905 905 CL CL . 
Q 6 CL B 1 906 906 CL CL . 
R 6 CL B 1 907 907 CL CL . 
S 6 CL B 1 908 908 CL CL . 
T 7 HOH A 1 1001 1008 HOH HOH . 
T 7 HOH A 2 1002 1010 HOH HOH . 
T 7 HOH A 3 1003 1013 HOH HOH . 
T 7 HOH A 4 1004 1007 HOH HOH . 
T 7 HOH A 5 1005 1011 HOH HOH . 
T 7 HOH A 6 1006 1005 HOH HOH . 
T 7 HOH A 7 1007 1009 HOH HOH . 
T 7 HOH A 8 1008 1024 HOH HOH . 
T 7 HOH A 9 1009 1001 HOH HOH . 
T 7 HOH A 10 1010 1002 HOH HOH . 
T 7 HOH A 11 1011 1003 HOH HOH . 
T 7 HOH A 12 1012 1004 HOH HOH . 
T 7 HOH A 13 1013 1015 HOH HOH . 
T 7 HOH A 14 1014 1012 HOH HOH . 
T 7 HOH A 15 1015 1014 HOH HOH . 
T 7 HOH A 16 1016 1006 HOH HOH . 
U 7 HOH B 1 1001 1027 HOH HOH . 
U 7 HOH B 2 1002 1026 HOH HOH . 
U 7 HOH B 3 1003 1001 HOH HOH . 
U 7 HOH B 4 1004 1022 HOH HOH . 
U 7 HOH B 5 1005 1030 HOH HOH . 
U 7 HOH B 6 1006 1016 HOH HOH . 
U 7 HOH B 7 1007 1005 HOH HOH . 
U 7 HOH B 8 1008 1002 HOH HOH . 
U 7 HOH B 9 1009 1020 HOH HOH . 
U 7 HOH B 10 1010 1023 HOH HOH . 
U 7 HOH B 11 1011 1017 HOH HOH . 
U 7 HOH B 12 1012 1018 HOH HOH . 
U 7 HOH B 13 1013 1012 HOH HOH . 
U 7 HOH B 14 1014 1032 HOH HOH . 
U 7 HOH B 15 1015 1006 HOH HOH . 
U 7 HOH B 16 1016 1003 HOH HOH . 
U 7 HOH B 17 1017 1011 HOH HOH . 
U 7 HOH B 18 1018 1014 HOH HOH . 
U 7 HOH B 19 1019 1010 HOH HOH . 
U 7 HOH B 20 1020 1009 HOH HOH . 
U 7 HOH B 21 1021 1007 HOH HOH . 
U 7 HOH B 22 1022 1031 HOH HOH . 
U 7 HOH B 23 1023 1025 HOH HOH . 
U 7 HOH B 24 1024 1019 HOH HOH . 
U 7 HOH B 25 1025 1015 HOH HOH . 
U 7 HOH B 26 1026 1029 HOH HOH . 
U 7 HOH B 27 1027 1008 HOH HOH . 
U 7 HOH B 28 1028 1021 HOH HOH . 
U 7 HOH B 29 1029 1004 HOH HOH . 
U 7 HOH B 30 1030 1028 HOH HOH . 
U 7 HOH B 31 1031 1013 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 P AMP . . . D 3 5.322 41.972 67.107 1 202.23 ? P AMP 902 A 1 
HETATM 2 O O1P AMP . . . D 3 6.21 42.199 65.905 1 200.38 ? O1P AMP 902 A 1 
HETATM 3 O O2P AMP . . . D 3 4.49 40.712 67.15 1 204 ? O2P AMP 902 A 1 
HETATM 4 O O3P AMP . . . D 3 6.149 42.063 68.367 1 202.48 ? O3P AMP 902 A 1 
HETATM 5 O O5' AMP . . . D 3 4.382 43.245 67.326 1 152.57 ? O5' AMP 902 A 1 
HETATM 6 C C5' AMP . . . D 3 3.393 43.255 68.354 1 153.16 ? C5' AMP 902 A 1 
HETATM 7 C C4' AMP . . . D 3 2.188 44.091 67.979 1 152.63 ? C4' AMP 902 A 1 
HETATM 8 O O4' AMP . . . D 3 1.723 43.705 66.662 1 146.24 ? O4' AMP 902 A 1 
HETATM 9 C C3' AMP . . . D 3 0.99 43.953 68.9 1 157.04 ? C3' AMP 902 A 1 
HETATM 10 O O3' AMP . . . D 3 0.21 45.152 68.866 1 160.48 ? O3' AMP 902 A 1 
HETATM 11 C C2' AMP . . . D 3 0.204 42.801 68.266 1 152.94 ? C2' AMP 902 A 1 
HETATM 12 O O2' AMP . . . D 3 -1.189 42.848 68.491 1 155.28 ? O2' AMP 902 A 1 
HETATM 13 C C1' AMP . . . D 3 0.55 42.908 66.767 1 144.88 ? C1' AMP 902 A 1 
HETATM 14 N N9 AMP . . . D 3 0.835 41.611 66.133 1 142 ? N9 AMP 902 A 1 
HETATM 15 C C8 AMP . . . D 3 2.078 41.148 65.933 1 141.27 ? C8 AMP 902 A 1 
HETATM 16 N N7 AMP . . . D 3 2.042 39.935 65.337 1 139.76 ? N7 AMP 902 A 1 
HETATM 17 C C5 AMP . . . D 3 0.743 39.625 65.146 1 141.49 ? C5 AMP 902 A 1 
HETATM 18 C C6 AMP . . . D 3 0.111 38.516 64.585 1 137.65 ? C6 AMP 902 A 1 
HETATM 19 N N6 AMP . . . D 3 0.841 37.48 64.098 1 133.77 ? N6 AMP 902 A 1 
HETATM 20 N N1 AMP . . . D 3 -1.239 38.488 64.531 1 136.31 ? N1 AMP 902 A 1 
HETATM 21 C C2 AMP . . . D 3 -1.961 39.512 65.015 1 136.82 ? C2 AMP 902 A 1 
HETATM 22 N N3 AMP . . . D 3 -1.375 40.593 65.564 1 140.91 ? N3 AMP 902 A 1 
HETATM 23 C C4 AMP . . . D 3 -0.018 40.685 65.642 1 143.1 ? C4 AMP 902 A 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           698 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           23 
#