data_474D
#
_model_server_result.job_id            CrgV9HehxpZ5FE5fKav3Cw 
_model_server_result.datetime_utc      '2025-01-11 09:46:57' 
_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          474d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":44}' 
#
_entry.id    474D 
#
_exptl.entry_id    474D 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              430.464 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            NETROPSIN 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         86.01 
_cell.angle_beta          84.37 
_cell.angle_gamma         68.9 
_cell.entry_id            474D 
_cell.length_a            32.66 
_cell.length_b            32.77 
_cell.length_c            37.71 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 474D 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 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
? dimeric 2 author_defined_assembly 1 
? dimeric 2 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F,I,J 1 1 
C,D,G,H,K,L 2 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
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H 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 A O3' DC 3 A DC 3 1_555 A P CBR 4 A CBR 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? 
covale ? covale2 A O3' CBR 4 A CBR 4 1_555 A P DC 5 A DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.577 ? 
covale ? covale3 B O3' DC 3 B DC 13 1_555 B P CBR 4 B CBR 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.615 ? 
covale ? covale4 B O3' CBR 4 B CBR 14 1_555 B P DC 5 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.59 ? 
covale ? covale5 C O3' DC 3 C DC 23 1_555 C P CBR 4 C CBR 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? 
covale ? covale6 C O3' CBR 4 C CBR 24 1_555 C P DC 5 C DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.589 ? 
covale ? covale7 D O3' DC 3 D DC 33 1_555 D P CBR 4 D CBR 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.586 ? 
covale ? covale8 D O3' CBR 4 D CBR 34 1_555 D P DC 5 D DC 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.594 ? 
#
_chem_comp.formula           'C18 H26 N10 O3' 
_chem_comp.formula_weight    430.464 
_chem_comp.id                NT 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              NETROPSIN 
_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
C1 N1 NT doub 110 n n 
C1 N2 NT sing 111 n n 
C1 N3 NT sing 112 n n 
N1 HN1 NT sing 113 n n 
N2 HN21 NT sing 114 n n 
N2 HN22 NT sing 115 n n 
N3 C2 NT sing 116 n n 
N3 HN3 NT sing 117 n n 
C2 C3 NT sing 118 n n 
C2 H21 NT sing 119 n n 
C2 H22 NT sing 120 n n 
C3 O1 NT doub 121 n n 
C3 N4 NT sing 122 n n 
N4 C4 NT sing 123 n n 
N4 HN4 NT sing 124 n n 
C4 C5 NT sing 125 n y 
C4 C7 NT doub 126 n y 
C5 C6 NT doub 127 n y 
C5 H5 NT sing 128 n n 
C6 N5 NT sing 129 n y 
C6 C9 NT sing 130 n n 
N5 C8 NT sing 131 n n 
N5 C7 NT sing 132 n y 
C8 H81 NT sing 133 n n 
C8 H82 NT sing 134 n n 
C8 H83 NT sing 135 n n 
C7 H7 NT sing 136 n n 
C9 O2 NT doub 137 n n 
C9 N6 NT sing 138 n n 
N6 C10 NT sing 139 n n 
N6 HN6 NT sing 140 n n 
C10 C11 NT sing 141 n y 
C10 C13 NT doub 142 n y 
C11 C12 NT doub 143 n y 
C11 H11 NT sing 144 n n 
C12 N7 NT sing 145 n y 
C12 C15 NT sing 146 n n 
N7 C14 NT sing 147 n n 
N7 C13 NT sing 148 n y 
C14 H141 NT sing 149 n n 
C14 H142 NT sing 150 n n 
C14 H143 NT sing 151 n n 
C13 H13 NT sing 152 n n 
C15 O3 NT doub 153 n n 
C15 N8 NT sing 154 n n 
N8 C16 NT sing 155 n n 
N8 HN8 NT sing 156 n n 
C16 C17 NT sing 157 n n 
C16 H161 NT sing 158 n n 
C16 H162 NT sing 159 n n 
C17 C18 NT sing 160 n n 
C17 H171 NT sing 161 n n 
C17 H172 NT sing 162 n n 
C18 N9 NT doub 163 n n 
C18 N10 NT sing 164 n n 
N9 HN9 NT sing 165 n n 
N10 HN01 NT sing 166 n n 
N10 HN02 NT sing 167 n n 
#
_atom_sites.entry_id                     474D 
_atom_sites.fract_transf_matrix[1][1]    0.030618 
_atom_sites.fract_transf_matrix[1][2]    -0.011815 
_atom_sites.fract_transf_matrix[1][3]    -0.002584 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.032709 
_atom_sites.fract_transf_matrix[2][3]    -0.001208 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.026665 
_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 NT A 1 41 41 NT NT . 
F 2 NT A 1 42 42 NT NT . 
G 2 NT C 1 43 43 NT NT . 
H 2 NT C 1 44 44 NT NT . 
I 3 HOH A 1 46 46 HOH HOH . 
I 3 HOH A 2 49 49 HOH HOH . 
I 3 HOH A 3 50 50 HOH HOH . 
I 3 HOH A 4 52 52 HOH HOH . 
I 3 HOH A 5 55 55 HOH HOH . 
I 3 HOH A 6 60 60 HOH HOH . 
I 3 HOH A 7 61 61 HOH HOH . 
I 3 HOH A 8 65 65 HOH HOH . 
I 3 HOH A 9 66 66 HOH HOH . 
I 3 HOH A 10 74 74 HOH HOH . 
I 3 HOH A 11 75 75 HOH HOH . 
I 3 HOH A 12 76 76 HOH HOH . 
I 3 HOH A 13 77 77 HOH HOH . 
I 3 HOH A 14 82 82 HOH HOH . 
J 3 HOH B 1 47 47 HOH HOH . 
J 3 HOH B 2 48 48 HOH HOH . 
J 3 HOH B 3 51 51 HOH HOH . 
J 3 HOH B 4 57 57 HOH HOH . 
J 3 HOH B 5 63 63 HOH HOH . 
J 3 HOH B 6 64 64 HOH HOH . 
J 3 HOH B 7 71 71 HOH HOH . 
J 3 HOH B 8 73 73 HOH HOH . 
J 3 HOH B 9 78 78 HOH HOH . 
J 3 HOH B 10 81 81 HOH HOH . 
K 3 HOH C 1 45 45 HOH HOH . 
K 3 HOH C 2 53 53 HOH HOH . 
K 3 HOH C 3 54 54 HOH HOH . 
K 3 HOH C 4 56 56 HOH HOH . 
K 3 HOH C 5 59 59 HOH HOH . 
K 3 HOH C 6 62 62 HOH HOH . 
K 3 HOH C 7 68 68 HOH HOH . 
K 3 HOH C 8 69 69 HOH HOH . 
K 3 HOH C 9 70 70 HOH HOH . 
K 3 HOH C 10 72 72 HOH HOH . 
K 3 HOH C 11 79 79 HOH HOH . 
L 3 HOH D 1 58 58 HOH HOH . 
L 3 HOH D 2 67 67 HOH HOH . 
L 3 HOH D 3 80 80 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 C C1 NT . . . H 2 -1.889 11.842 17.582 1 54.64 ? C1 NT 44 C 1 
HETATM 2 N N1 NT . . . H 2 -2.919 12.689 17.696 1 55.87 ? N1 NT 44 C 1 
HETATM 3 N N2 NT . . . H 2 -1.019 11.812 18.606 1 55.42 ? N2 NT 44 C 1 
HETATM 4 N N3 NT . . . H 2 -1.784 11.047 16.495 1 53.17 ? N3 NT 44 C 1 
HETATM 5 C C2 NT . . . H 2 -2.955 10.49 15.834 1 49.22 ? C2 NT 44 C 1 
HETATM 6 C C3 NT . . . H 2 -2.471 9.564 14.741 1 47.09 ? C3 NT 44 C 1 
HETATM 7 O O1 NT . . . H 2 -3.037 9.875 13.724 1 46.36 ? O1 NT 44 C 1 
HETATM 8 N N4 NT . . . H 2 -1.56 8.585 14.821 1 45.32 ? N4 NT 44 C 1 
HETATM 9 C C4 NT . . . H 2 -1.156 7.712 13.802 1 43.93 ? C4 NT 44 C 1 
HETATM 10 C C5 NT . . . H 2 -0.39 6.571 13.967 1 42.9 ? C5 NT 44 C 1 
HETATM 11 C C6 NT . . . H 2 -0.178 5.902 12.791 1 41.46 ? C6 NT 44 C 1 
HETATM 12 N N5 NT . . . H 2 -0.805 6.605 11.845 1 42.67 ? N5 NT 44 C 1 
HETATM 13 C C8 NT . . . H 2 -0.87 6.293 10.335 1 42.91 ? C8 NT 44 C 1 
HETATM 14 C C7 NT . . . H 2 -1.4 7.684 12.404 1 43.49 ? C7 NT 44 C 1 
HETATM 15 C C9 NT . . . H 2 0.559 4.722 12.444 1 40.65 ? C9 NT 44 C 1 
HETATM 16 O O2 NT . . . H 2 0.936 4.609 11.292 1 40.91 ? O2 NT 44 C 1 
HETATM 17 N N6 NT . . . H 2 0.796 3.81 13.382 1 40.57 ? N6 NT 44 C 1 
HETATM 18 C C10 NT . . . H 2 1.639 2.751 13.073 1 40.63 ? C10 NT 44 C 1 
HETATM 19 C C11 NT . . . H 2 1.965 1.612 13.778 1 41.3 ? C11 NT 44 C 1 
HETATM 20 C C12 NT . . . H 2 2.898 0.856 13.108 1 42.25 ? C12 NT 44 C 1 
HETATM 21 N N7 NT . . . H 2 3.154 1.548 11.964 1 42.34 ? N7 NT 44 C 1 
HETATM 22 C C14 NT . . . H 2 4.083 1.303 10.747 1 43.7 ? C14 NT 44 C 1 
HETATM 23 C C13 NT . . . H 2 2.433 2.66 11.918 1 40.92 ? C13 NT 44 C 1 
HETATM 24 C C15 NT . . . H 2 3.543 -0.418 13.417 1 43.35 ? C15 NT 44 C 1 
HETATM 25 O O3 NT . . . H 2 4.329 -0.891 12.625 1 44.28 ? O3 NT 44 C 1 
HETATM 26 N N8 NT . . . H 2 3.273 -1.109 14.523 1 44.66 ? N8 NT 44 C 1 
HETATM 27 C C16 NT . . . H 2 3.976 -2.367 14.712 1 46.85 ? C16 NT 44 C 1 
HETATM 28 C C17 NT . . . H 2 5.046 -3.078 13.875 1 49.18 ? C17 NT 44 C 1 
HETATM 29 C C18 NT . . . H 2 5.901 -4.163 14.549 1 51.74 ? C18 NT 44 C 1 
HETATM 30 N N9 NT . . . H 2 7.054 -4.586 13.983 1 52.77 ? N9 NT 44 C 1 
HETATM 31 N N10 NT . . . H 2 5.464 -4.635 15.735 1 52.12 ? N10 NT 44 C 1 
#
_model_server_stats.io_time_ms              27 
_model_server_stats.parse_time_ms           5 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           295 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           31 
#