data_9MED
#
_model_server_result.job_id            A9n3xMFywMBnKlozo3ZlFA 
_model_server_result.datetime_utc      '2024-12-22 03:24:44' 
_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          9med 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":501}' 
#
_entry.id    9MED 
#
_exptl.entry_id    9MED 
_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    4 
_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            9MED 
_cell.length_a            86.875 
_cell.length_b            86.875 
_cell.length_c            475.979 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9MED 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,V,W,X,Y,Z 
_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
? 3 F N N 
? 3 J N N 
? 3 P N N 
? 3 U N N 
#
_struct_conn.conn_type_id                   metalc 
_struct_conn.details                        ? 
_struct_conn.id                             metalc1 
_struct_conn.ptnr1_label_asym_id            G 
_struct_conn.ptnr1_label_atom_id            O32 
_struct_conn.ptnr1_label_comp_id            PPV 
_struct_conn.ptnr1_label_seq_id             . 
_struct_conn.ptnr1_auth_asym_id             A 
_struct_conn.ptnr1_auth_comp_id             PPV 
_struct_conn.ptnr1_auth_seq_id              503 
_struct_conn.ptnr1_symmetry                 1_555 
_struct_conn.ptnr2_label_asym_id            I 
_struct_conn.ptnr2_label_atom_id            MG 
_struct_conn.ptnr2_label_comp_id            MG 
_struct_conn.ptnr2_label_seq_id             . 
_struct_conn.ptnr2_auth_asym_id             A 
_struct_conn.ptnr2_auth_comp_id             MG 
_struct_conn.ptnr2_auth_seq_id              505 
_struct_conn.ptnr2_symmetry                 1_555 
_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                2.846 
_struct_conn.pdbx_value_order               ? 
#
_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                     9MED 
_atom_sites.fract_transf_matrix[1][1]    0.011511 
_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]    0.011511 
_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]    0.002101 
_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 PO4 A 1 501 1 PO4 PO4 . 
F 3 AMP A 1 502 101 AMP AMP . 
G 4 PPV A 1 503 301 PPV PPV . 
H 2 PO4 A 1 504 407 PO4 PO4 . 
I 5 MG A 1 505 601 MG MG . 
J 3 AMP B 1 501 104 AMP AMP . 
K 6 BG6 B 1 502 202 BG6 BG6 . 
L 2 PO4 B 1 503 401 PO4 PO4 . 
M 2 PO4 B 1 504 403 PO4 PO4 . 
N 2 PO4 B 1 505 404 PO4 PO4 . 
O 7 CL C 1 501 1 CL CL . 
P 3 AMP C 1 502 103 AMP AMP . 
Q 6 BG6 C 1 503 201 BG6 BG6 . 
R 2 PO4 C 1 504 402 PO4 PO4 . 
S 2 PO4 C 1 505 405 PO4 PO4 . 
T 2 PO4 C 1 506 408 PO4 PO4 . 
U 3 AMP D 1 501 102 AMP AMP . 
V 2 PO4 D 1 502 406 PO4 PO4 . 
W 8 HOH A 1 601 16 HOH HOH . 
W 8 HOH A 2 602 8 HOH HOH . 
X 8 HOH B 1 601 2 HOH HOH . 
X 8 HOH B 2 602 15 HOH HOH . 
X 8 HOH B 3 603 3 HOH HOH . 
X 8 HOH B 4 604 7 HOH HOH . 
Y 8 HOH C 1 601 9 HOH HOH . 
Y 8 HOH C 2 602 4 HOH HOH . 
Y 8 HOH C 3 603 13 HOH HOH . 
Y 8 HOH C 4 604 17 HOH HOH . 
Y 8 HOH C 5 605 14 HOH HOH . 
Z 8 HOH D 1 601 12 HOH HOH . 
Z 8 HOH D 2 602 6 HOH HOH . 
Z 8 HOH D 3 603 5 HOH HOH . 
Z 8 HOH D 4 604 11 HOH HOH . 
Z 8 HOH D 5 605 1 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 . . . J 3 19.598 -6.841 -60.942 1 99.45 ? P AMP 501 B 1 
HETATM 2 O O1P AMP . . . J 3 18.321 -7.171 -60.209 1 88.08 ? O1P AMP 501 B 1 
HETATM 3 O O2P AMP . . . J 3 20.346 -8.05 -61.452 1 93.35 ? O2P AMP 501 B 1 
HETATM 4 O O3P AMP . . . J 3 19.494 -5.709 -61.938 1 83.6 ? O3P AMP 501 B 1 
HETATM 5 O O5' AMP . . . J 3 20.55 -6.257 -59.807 1 90.89 ? O5' AMP 501 B 1 
HETATM 6 C C5' AMP . . . J 3 21.894 -5.895 -60.106 1 80.45 ? C5' AMP 501 B 1 
HETATM 7 C C4' AMP . . . J 3 22.77 -5.919 -58.879 1 82.55 ? C4' AMP 501 B 1 
HETATM 8 O O4' AMP . . . J 3 22.562 -4.701 -58.121 1 83.75 ? O4' AMP 501 B 1 
HETATM 9 C C3' AMP . . . J 3 22.519 -7.084 -57.921 1 80.05 ? C3' AMP 501 B 1 
HETATM 10 O O3' AMP . . . J 3 23.764 -7.635 -57.49 1 80.14 ? O3' AMP 501 B 1 
HETATM 11 C C2' AMP . . . J 3 21.787 -6.438 -56.741 1 84.68 ? C2' AMP 501 B 1 
HETATM 12 O O2' AMP . . . J 3 22.029 -7.062 -55.495 1 94.98 ? O2' AMP 501 B 1 
HETATM 13 C C1' AMP . . . J 3 22.319 -5.01 -56.766 1 80.86 ? C1' AMP 501 B 1 
HETATM 14 N N9 AMP . . . J 3 21.387 -4 -56.252 1 86.9 ? N9 AMP 501 B 1 
HETATM 15 C C8 AMP . . . J 3 20.07 -3.931 -56.537 1 91.27 ? C8 AMP 501 B 1 
HETATM 16 N N7 AMP . . . J 3 19.495 -2.871 -55.916 1 86.18 ? N7 AMP 501 B 1 
HETATM 17 C C5 AMP . . . J 3 20.458 -2.239 -55.226 1 80.3 ? C5 AMP 501 B 1 
HETATM 18 C C6 AMP . . . J 3 20.523 -1.05 -54.355 1 82.13 ? C6 AMP 501 B 1 
HETATM 19 N N6 AMP . . . J 3 19.402 -0.333 -54.121 1 78.87 ? N6 AMP 501 B 1 
HETATM 20 N N1 AMP . . . J 3 21.72 -0.714 -53.823 1 76.91 ? N1 AMP 501 B 1 
HETATM 21 C C2 AMP . . . J 3 22.831 -1.435 -54.065 1 74.51 ? C2 AMP 501 B 1 
HETATM 22 N N3 AMP . . . J 3 22.835 -2.531 -54.85 1 88.53 ? N3 AMP 501 B 1 
HETATM 23 C C4 AMP . . . J 3 21.704 -2.981 -55.447 1 75.55 ? C4 AMP 501 B 1 
#
_model_server_stats.io_time_ms              37 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    33 
_model_server_stats.query_time_ms           348 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           23 
#