data_3NP6
#
_model_server_result.job_id            BXma-BCdn1uhPmphcdIeXw 
_model_server_result.datetime_utc      '2024-10-15 00:24:42' 
_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          3np6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":7}' 
#
_entry.id    3NP6 
#
_exptl.entry_id    3NP6 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              336.361 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            BERBERINE 
_entity.pdbx_number_of_molecules    1 
_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         120 
_cell.entry_id            3NP6 
_cell.length_a            30.37 
_cell.length_b            30.37 
_cell.length_c            118.26 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3NP6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32 2 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
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_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 1 1 
C,D,F,G 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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             F 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 E CA CA . B CA 1 1_555 B OP1 DG 6 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? 
metalc ? metalc2 E CA CA . B CA 1 1_555 D OP1 DG 6 D DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? 
hydrog WATSON-CRICK hydrog1 A N1 DG 2 A DG 2 1_555 B N3 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A N2 DG 2 A DG 2 1_555 B O2 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A O6 DG 2 A DG 2 1_555 B N4 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog TYPE_4_PAIR hydrog4 A N2 DG 2 A DG 2 1_555 D N3 DG 6 D DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog TYPE_4_PAIR hydrog5 A N3 DG 2 A DG 2 1_555 D N2 DG 6 D DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 A N3 DT 3 A DT 3 1_555 B N1 DA 4 B DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 A O4 DT 3 A DT 3 1_555 B N6 DA 4 B DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 A N1 DA 4 A DA 4 1_555 B N3 DT 3 B DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 A N6 DA 4 A DA 4 1_555 B O4 DT 3 B DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 A N3 DC 5 A DC 5 1_555 B N1 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog11 A N4 DC 5 A DC 5 1_555 B O6 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog12 A O2 DC 5 A DC 5 1_555 B N2 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog TYPE_4_PAIR hydrog13 B N2 DG 6 B DG 12 1_555 C N3 DG 2 C DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog TYPE_4_PAIR hydrog14 B N3 DG 6 B DG 12 1_555 C N2 DG 2 C DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog15 C N1 DG 2 C DG 2 1_555 D N3 DC 5 D DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog16 C N2 DG 2 C DG 2 1_555 D O2 DC 5 D DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog17 C O6 DG 2 C DG 2 1_555 D N4 DC 5 D DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog18 C N3 DT 3 C DT 3 1_555 D N1 DA 4 D DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog19 C O4 DT 3 C DT 3 1_555 D N6 DA 4 D DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog20 C N1 DA 4 C DA 4 1_555 D N3 DT 3 D DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog21 C N6 DA 4 C DA 4 1_555 D O4 DT 3 D DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog22 C N3 DC 5 C DC 5 1_555 D N1 DG 2 D DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog23 C N4 DC 5 C DC 5 1_555 D O6 DG 2 D DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog24 C O2 DC 5 C DC 5 1_555 D N2 DG 2 D DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_chem_comp.formula           'C20 H18 N O4 1' 
_chem_comp.formula_weight    336.361 
_chem_comp.id                BER 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              BERBERINE 
_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 C2 BER sing 1 n y 
C1 N1 BER doub 2 n y 
C1 C3 BER sing 3 n y 
C2 C4 BER doub 4 n y 
C2 C5 BER sing 5 n y 
N1 C6 BER sing 6 n y 
N1 C7 BER sing 7 n n 
C3 C8 BER doub 8 n y 
C3 H31 BER sing 9 n n 
C4 C9 BER sing 10 n y 
C4 C10 BER sing 11 n n 
C5 C11 BER doub 12 n y 
C5 H51 BER sing 13 n n 
C6 C12 BER doub 14 n y 
C6 H61 BER sing 15 n n 
C7 C10 BER sing 16 n n 
C7 H71 BER sing 17 n n 
C7 H72 BER sing 18 n n 
C8 C12 BER sing 19 n y 
C8 C13 BER sing 20 n y 
C9 C14 BER doub 21 n y 
C9 H91 BER sing 22 n n 
C10 H101 BER sing 23 n n 
C10 H102 BER sing 24 n n 
C11 C14 BER sing 25 n y 
C11 O1 BER sing 26 n n 
C12 C15 BER sing 27 n y 
C13 C16 BER doub 28 n y 
C13 H131 BER sing 29 n n 
C14 O2 BER sing 30 n n 
O1 C17 BER sing 31 n n 
C15 C18 BER doub 32 n y 
C15 O3 BER sing 33 n n 
C16 C18 BER sing 34 n y 
C16 H161 BER sing 35 n n 
O2 C17 BER sing 36 n n 
C17 H171 BER sing 37 n n 
C17 H172 BER sing 38 n n 
C18 O4 BER sing 39 n n 
O3 C19 BER sing 40 n n 
O4 C20 BER sing 41 n n 
C19 H191 BER sing 42 n n 
C19 H192 BER sing 43 n n 
C19 H193 BER sing 44 n n 
C20 H201 BER sing 45 n n 
C20 H202 BER sing 46 n n 
C20 H203 BER sing 47 n n 
#
_atom_sites.entry_id                     3NP6 
_atom_sites.fract_transf_matrix[1][1]    0.032927 
_atom_sites.fract_transf_matrix[1][2]    0.019011 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.038021 
_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]    0.008456 
_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 CA B 1 1 1 CA CA . 
F 3 BER C 1 7 1 BER BER . 
G 4 HOH D 1 1 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 C C1 BER . . . F 3 22.371 25.635 11.021 1 18.98 ? C1 BER 7 C 1 
HETATM 2 C C2 BER . . . F 3 21.552 26.387 12.005 1 18.81 ? C2 BER 7 C 1 
HETATM 3 N N1 BER . . . F 3 22.251 25.914 9.631 1 19.01 ? N1 BER 7 C 1 
HETATM 4 C C3 BER . . . F 3 23.315 24.721 11.496 1 19.07 ? C3 BER 7 C 1 
HETATM 5 C C4 BER . . . F 3 20.514 27.351 11.53 1 18.59 ? C4 BER 7 C 1 
HETATM 6 C C5 BER . . . F 3 21.894 26.28 13.356 1 18.38 ? C5 BER 7 C 1 
HETATM 7 C C6 BER . . . F 3 23.039 25.271 8.734 1 19.33 ? C6 BER 7 C 1 
HETATM 8 C C7 BER . . . F 3 21.276 26.894 9.108 1 18.93 ? C7 BER 7 C 1 
HETATM 9 C C8 BER . . . F 3 24.132 24.046 10.598 1 19.57 ? C8 BER 7 C 1 
HETATM 10 C C9 BER . . . F 3 19.761 28.086 12.451 1 17.85 ? C9 BER 7 C 1 
HETATM 11 C C10 BER . . . F 3 20.194 27.44 10.052 1 18.67 ? C10 BER 7 C 1 
HETATM 12 C C11 BER . . . F 3 21.151 27.035 14.239 1 18.42 ? C11 BER 7 C 1 
HETATM 13 C C12 BER . . . F 3 23.992 24.328 9.144 1 19.61 ? C12 BER 7 C 1 
HETATM 14 C C13 BER . . . F 3 25.071 23.124 11.049 1 19.61 ? C13 BER 7 C 1 
HETATM 15 C C14 BER . . . F 3 20.096 27.934 13.789 1 18.21 ? C14 BER 7 C 1 
HETATM 16 O O1 BER . . . F 3 21.239 27.111 15.592 1 19.34 ? O1 BER 7 C 1 
HETATM 17 C C15 BER . . . F 3 24.89 23.595 8.197 1 20.63 ? C15 BER 7 C 1 
HETATM 18 C C16 BER . . . F 3 25.9 22.433 10.164 1 20.18 ? C16 BER 7 C 1 
HETATM 19 O O2 BER . . . F 3 19.572 28.528 14.896 1 19.35 ? O2 BER 7 C 1 
HETATM 20 C C17 BER . . . F 3 20.287 28.082 16.068 1 19.16 ? C17 BER 7 C 1 
HETATM 21 C C18 BER . . . F 3 25.861 22.604 8.778 1 20.95 ? C18 BER 7 C 1 
HETATM 22 O O3 BER . . . F 3 24.755 23.824 6.849 1 22.47 ? O3 BER 7 C 1 
HETATM 23 O O4 BER . . . F 3 26.767 21.838 8.062 1 22.88 ? O4 BER 7 C 1 
HETATM 24 C C19 BER . . . F 3 25.824 24.241 5.997 1 22.09 ? C19 BER 7 C 1 
HETATM 25 C C20 BER . . . F 3 26.545 21.227 6.784 1 24.23 ? C20 BER 7 C 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           351 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           25 
#