data_5GTD
#
_model_server_result.job_id            xKXukdgcNi-eP2ci17lRqQ 
_model_server_result.datetime_utc      '2024-12-24 17:36:36' 
_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          5gtd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":504}' 
#
_entry.id    5GTD 
#
_exptl.entry_id    5GTD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              347.221 
_entity.id                          4 
_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            5GTD 
_cell.length_a            121.814 
_cell.length_b            121.814 
_cell.length_c            98.563 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5GTD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        78 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 43' 
#
_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,I,J,K,L,M,N,O 
_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
? 4 G N N 
? 4 L 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
covale ? covale1 G P AMP . A AMP 505 1_555 H O5 OSB . A OSB 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.595 ? 
covale ? covale2 L P AMP . B AMP 504 1_555 M O4 OSB . B OSB 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.596 ? 
metalc ? metalc1 B O PRO 8 B PRO 6 1_555 J MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.902 ? 
metalc ? metalc2 B OE1 GLN 13 B GLN 11 1_555 J MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.851 ? 
#
_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                     5GTD 
_atom_sites.fract_transf_matrix[1][1]    0.008209 
_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]    0.008209 
_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]    0.010146 
_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 CL A 1 501 2 CL CL . 
D 2 CL A 1 502 5 CL CL . 
E 2 CL A 1 503 6 CL CL . 
F 3 PEG A 1 504 1 PEG PEG . 
G 4 AMP A 1 505 500 AMP DRG . 
H 5 OSB A 1 506 500 OSB DRG . 
I 2 CL B 1 501 3 CL CL . 
J 6 MG B 1 502 2 MG MG . 
K 7 IMD B 1 503 1 IMD IMD . 
L 4 AMP B 1 504 500 AMP DRG . 
M 5 OSB B 1 505 500 OSB DRG . 
N 8 HOH A 1 601 18 HOH HOH . 
N 8 HOH A 2 602 17 HOH HOH . 
N 8 HOH A 3 603 11 HOH HOH . 
N 8 HOH A 4 604 7 HOH HOH . 
N 8 HOH A 5 605 8 HOH HOH . 
N 8 HOH A 6 606 36 HOH HOH . 
N 8 HOH A 7 607 10 HOH HOH . 
N 8 HOH A 8 608 6 HOH HOH . 
N 8 HOH A 9 609 12 HOH HOH . 
N 8 HOH A 10 610 51 HOH HOH . 
N 8 HOH A 11 611 22 HOH HOH . 
N 8 HOH A 12 612 20 HOH HOH . 
N 8 HOH A 13 613 14 HOH HOH . 
N 8 HOH A 14 614 43 HOH HOH . 
N 8 HOH A 15 615 47 HOH HOH . 
N 8 HOH A 16 616 40 HOH HOH . 
N 8 HOH A 17 617 25 HOH HOH . 
N 8 HOH A 18 618 48 HOH HOH . 
N 8 HOH A 19 619 53 HOH HOH . 
N 8 HOH A 20 620 54 HOH HOH . 
N 8 HOH A 21 621 33 HOH HOH . 
N 8 HOH A 22 622 1 HOH HOH . 
N 8 HOH A 23 623 35 HOH HOH . 
N 8 HOH A 24 624 49 HOH HOH . 
N 8 HOH A 25 625 9 HOH HOH . 
N 8 HOH A 26 626 38 HOH HOH . 
N 8 HOH A 27 627 13 HOH HOH . 
O 8 HOH B 1 601 28 HOH HOH . 
O 8 HOH B 2 602 21 HOH HOH . 
O 8 HOH B 3 603 2 HOH HOH . 
O 8 HOH B 4 604 39 HOH HOH . 
O 8 HOH B 5 605 3 HOH HOH . 
O 8 HOH B 6 606 44 HOH HOH . 
O 8 HOH B 7 607 5 HOH HOH . 
O 8 HOH B 8 608 4 HOH HOH . 
O 8 HOH B 9 609 50 HOH HOH . 
O 8 HOH B 10 610 24 HOH HOH . 
O 8 HOH B 11 611 46 HOH HOH . 
O 8 HOH B 12 612 15 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 . . . L 4 42.612 -124.514 20.226 1 101.82 ? P AMP 504 B 1 
HETATM 2 O O1P AMP . . . L 4 42.998 -123.1 20.473 1 97.9 ? O1P AMP 504 B 1 
HETATM 3 O O2P AMP . . . L 4 43.862 -125.218 20.58 1 100.17 ? O2P AMP 504 B 1 
HETATM 4 O O5' AMP . . . L 4 41.387 -124.97 21.188 1 105.75 ? O5' AMP 504 B 1 
HETATM 5 C C5' AMP . . . L 4 41.389 -126.313 21.716 1 105.25 ? C5' AMP 504 B 1 
HETATM 6 C C4' AMP . . . L 4 40.578 -126.363 22.947 1 109.17 ? C4' AMP 504 B 1 
HETATM 7 O O4' AMP . . . L 4 39.115 -126.239 22.597 1 110.54 ? O4' AMP 504 B 1 
HETATM 8 C C3' AMP . . . L 4 40.793 -127.653 23.632 1 108.85 ? C3' AMP 504 B 1 
HETATM 9 O O3' AMP . . . L 4 41.457 -127.425 24.927 1 111.55 ? O3' AMP 504 B 1 
HETATM 10 C C2' AMP . . . L 4 39.496 -128.281 23.848 1 111.46 ? C2' AMP 504 B 1 
HETATM 11 O O2' AMP . . . L 4 39.26 -128.431 25.267 1 114.83 ? O2' AMP 504 B 1 
HETATM 12 C C1' AMP . . . L 4 38.455 -127.417 23.259 1 113.17 ? C1' AMP 504 B 1 
HETATM 13 N N9 AMP . . . L 4 37.723 -128.14 22.311 1 116.3 ? N9 AMP 504 B 1 
HETATM 14 C C8 AMP . . . L 4 38.108 -128.299 20.94 1 114.57 ? C8 AMP 504 B 1 
HETATM 15 N N7 AMP . . . L 4 37.106 -129.084 20.354 1 112.55 ? N7 AMP 504 B 1 
HETATM 16 C C5 AMP . . . L 4 36.139 -129.401 21.317 1 115.94 ? C5 AMP 504 B 1 
HETATM 17 C C6 AMP . . . L 4 34.971 -130.125 21.294 1 118.59 ? C6 AMP 504 B 1 
HETATM 18 N N6 AMP . . . L 4 34.573 -130.795 20.105 1 114.85 ? N6 AMP 504 B 1 
HETATM 19 N N1 AMP . . . L 4 34.263 -130.247 22.379 1 121.48 ? N1 AMP 504 B 1 
HETATM 20 C C2 AMP . . . L 4 34.54 -129.747 23.52 1 121.83 ? C2 AMP 504 B 1 
HETATM 21 N N3 AMP . . . L 4 35.689 -128.999 23.667 1 121.33 ? N3 AMP 504 B 1 
HETATM 22 C C4 AMP . . . L 4 36.548 -128.787 22.571 1 118.39 ? C4 AMP 504 B 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    25 
_model_server_stats.query_time_ms           364 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           22 
#