data_1GPH
#
_model_server_result.job_id            9-Ln-Zp9qikM6tj5H53qWg 
_model_server_result.datetime_utc      '2024-11-08 11:31:46' 
_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          1gph 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":468}' 
#
_entry.id    1GPH 
#
_exptl.entry_id    1GPH 
_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    8 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          91.4 
_cell.angle_gamma         90 
_cell.entry_id            1GPH 
_cell.length_a            158.8 
_cell.length_b            75.7 
_cell.length_c            94.1 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1GPH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PQS tetrameric 4 author_and_software_defined_assembly 1 
PISA dimeric 2 software_defined_assembly 2 
PISA dimeric 2 software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P 1 1 
A,B,E,F,G,H,I,J 2 1 
C,D,K,L,M,N,O,P 3 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
? 3 F N N 
? 3 G N N 
? 3 I N N 
? 3 J N N 
? 3 L N N 
? 3 M N N 
? 3 O N N 
? 3 P 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 SG CYS 236 1 CYS 236 1_555 E FE2 SF4 . 1 SF4 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? 
metalc ? metalc2 A SG CYS 382 1 CYS 382 1_555 E FE4 SF4 . 1 SF4 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? 
metalc ? metalc3 A SG CYS 437 1 CYS 437 1_555 E FE1 SF4 . 1 SF4 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? 
metalc ? metalc4 A SG CYS 440 1 CYS 440 1_555 E FE3 SF4 . 1 SF4 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? 
metalc ? metalc5 B SG CYS 236 2 CYS 236 1_555 H FE2 SF4 . 2 SF4 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? 
metalc ? metalc6 B SG CYS 382 2 CYS 382 1_555 H FE4 SF4 . 2 SF4 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? 
metalc ? metalc7 B SG CYS 437 2 CYS 437 1_555 H FE1 SF4 . 2 SF4 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? 
metalc ? metalc8 B SG CYS 440 2 CYS 440 1_555 H FE3 SF4 . 2 SF4 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? 
metalc ? metalc9 C SG CYS 236 3 CYS 236 1_555 K FE2 SF4 . 3 SF4 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? 
metalc ? metalc10 C SG CYS 382 3 CYS 382 1_555 K FE4 SF4 . 3 SF4 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? 
metalc ? metalc11 C SG CYS 437 3 CYS 437 1_555 K FE1 SF4 . 3 SF4 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? 
metalc ? metalc12 C SG CYS 440 3 CYS 440 1_555 K FE3 SF4 . 3 SF4 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? 
metalc ? metalc13 D SG CYS 236 4 CYS 236 1_555 N FE2 SF4 . 4 SF4 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? 
metalc ? metalc14 D SG CYS 382 4 CYS 382 1_555 N FE4 SF4 . 4 SF4 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? 
metalc ? metalc15 D SG CYS 437 4 CYS 437 1_555 N FE1 SF4 . 4 SF4 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? 
metalc ? metalc16 D SG CYS 440 4 CYS 440 1_555 N FE3 SF4 . 4 SF4 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? 
#
_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                     1GPH 
_atom_sites.fract_transf_matrix[1][1]    0.006297 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000154 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01321 
_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]    0.01063 
_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
E 2 SF4 1 1 466 466 SF4 FS4 . 
F 3 AMP 1 1 467 467 AMP AMP . 
G 3 AMP 1 1 468 468 AMP AMP . 
H 2 SF4 2 1 466 466 SF4 FS4 . 
I 3 AMP 2 1 467 467 AMP AMP . 
J 3 AMP 2 1 468 468 AMP AMP . 
K 2 SF4 3 1 466 466 SF4 FS4 . 
L 3 AMP 3 1 467 467 AMP AMP . 
M 3 AMP 3 1 468 468 AMP AMP . 
N 2 SF4 4 1 466 466 SF4 FS4 . 
O 3 AMP 4 1 467 467 AMP AMP . 
P 3 AMP 4 1 468 468 AMP AMP . 
#
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 . . . M 3 93.368 17.509 15.479 1 19.21 ? P AMP 468 3 1 
HETATM 2 O O1P AMP . . . M 3 94.839 17.68 15.578 1 19.21 ? O1P AMP 468 3 1 
HETATM 3 O O2P AMP . . . M 3 92.921 16.514 14.485 1 19.21 ? O2P AMP 468 3 1 
HETATM 4 O O3P AMP . . . M 3 92.686 17.398 16.789 1 19.21 ? O3P AMP 468 3 1 
HETATM 5 O O5' AMP . . . M 3 92.917 18.938 14.887 1 19.21 ? O5' AMP 468 3 1 
HETATM 6 C C5' AMP . . . M 3 92.691 19.13 13.5 1 19.21 ? C5' AMP 468 3 1 
HETATM 7 C C4' AMP . . . M 3 91.278 19.592 13.352 1 19.21 ? C4' AMP 468 3 1 
HETATM 8 O O4' AMP . . . M 3 91.113 20.818 14.06 1 19.21 ? O4' AMP 468 3 1 
HETATM 9 C C3' AMP . . . M 3 90.889 19.812 11.934 1 19.21 ? C3' AMP 468 3 1 
HETATM 10 O O3' AMP . . . M 3 89.729 19.02 11.734 1 19.21 ? O3' AMP 468 3 1 
HETATM 11 C C2' AMP . . . M 3 90.638 21.297 11.881 1 19.21 ? C2' AMP 468 3 1 
HETATM 12 O O2' AMP . . . M 3 89.509 21.547 11.098 1 19.21 ? O2' AMP 468 3 1 
HETATM 13 C C1' AMP . . . M 3 90.378 21.75 13.282 1 19.21 ? C1' AMP 468 3 1 
HETATM 14 N N9 AMP . . . M 3 90.897 23.112 13.558 1 19.21 ? N9 AMP 468 3 1 
HETATM 15 C C8 AMP . . . M 3 92.057 23.671 13.13 1 19.21 ? C8 AMP 468 3 1 
HETATM 16 N N7 AMP . . . M 3 92.367 24.808 13.683 1 19.21 ? N7 AMP 468 3 1 
HETATM 17 C C5 AMP . . . M 3 91.356 25.025 14.598 1 19.21 ? C5 AMP 468 3 1 
HETATM 18 C C6 AMP . . . M 3 91.085 26.092 15.494 1 19.21 ? C6 AMP 468 3 1 
HETATM 19 N N6 AMP . . . M 3 91.906 27.1 15.747 1 19.21 ? N6 AMP 468 3 1 
HETATM 20 N N1 AMP . . . M 3 89.928 26.069 16.118 1 19.21 ? N1 AMP 468 3 1 
HETATM 21 C C2 AMP . . . M 3 89.198 24.963 16.024 1 19.21 ? C2 AMP 468 3 1 
HETATM 22 N N3 AMP . . . M 3 89.385 23.83 15.36 1 19.21 ? N3 AMP 468 3 1 
HETATM 23 C C4 AMP . . . M 3 90.485 23.96 14.581 1 19.21 ? C4 AMP 468 3 1 
#
_model_server_stats.io_time_ms              21 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    53 
_model_server_stats.query_time_ms           319 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           23 
#