data_6DM1
#
_model_server_result.job_id            Um5IUYiXckmrMLGKqZcUPg 
_model_server_result.datetime_utc      '2024-12-23 07:49:34' 
_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          6dm1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":1303}' 
#
_entry.id    6DM1 
#
_exptl.entry_id    6DM1 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              370.532 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            N-[3-({4-[(3-aminopropyl)amino]butyl}amino)propyl]-2-(naphthalen-1-yl)acetamide 
_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         90 
_cell.entry_id            6DM1 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6DM1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             K 
_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
disulf ? disulf1 A SG CYS 54 A CYS 63 1_555 A SG CYS 306 A CYS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf2 A SG CYS 709 A CYS 718 1_555 A SG CYS 764 A CYS 773 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf3 A SG CYS 858 A CYS 1039 1_555 A SG CYS 886 A CYS 1067 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf4 A SG CYS 885 A CYS 1066 1_555 A SG CYS 895 A CYS 1076 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf5 B SG CYS 54 B CYS 63 1_555 B SG CYS 306 B CYS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf6 B SG CYS 709 B CYS 718 1_555 B SG CYS 764 B CYS 773 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf7 B SG CYS 858 B CYS 1039 1_555 B SG CYS 886 B CYS 1067 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf8 B SG CYS 885 B CYS 1066 1_555 B SG CYS 895 B CYS 1076 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf9 C SG CYS 54 C CYS 63 1_555 C SG CYS 306 C CYS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf10 C SG CYS 709 C CYS 718 1_555 C SG CYS 764 C CYS 773 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf11 C SG CYS 858 C CYS 1039 1_555 C SG CYS 886 C CYS 1067 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf12 C SG CYS 885 C CYS 1066 1_555 C SG CYS 895 C CYS 1076 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf13 D SG CYS 54 D CYS 63 1_555 D SG CYS 306 D CYS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf14 D SG CYS 709 D CYS 718 1_555 D SG CYS 764 D CYS 773 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
disulf ? disulf15 D SG CYS 858 D CYS 1039 1_555 D SG CYS 886 D CYS 1067 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf16 D SG CYS 885 D CYS 1066 1_555 D SG CYS 895 D CYS 1076 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
#
_chem_comp.formula           'C22 H34 N4 O' 
_chem_comp.formula_weight    370.532 
_chem_comp.id                GYY 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              N-[3-({4-[(3-aminopropyl)amino]butyl}amino)propyl]-2-(naphthalen-1-yl)acetamide 
_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
NAU CAT GYY sing 172 n n 
CAT CAS GYY sing 173 n n 
CAS CAR GYY sing 174 n n 
CAR NAQ GYY sing 175 n n 
NAQ CAP GYY sing 176 n n 
CAP CAO GYY sing 177 n n 
CAO CAN GYY sing 178 n n 
CAN CAM GYY sing 179 n n 
CAM NAL GYY sing 180 n n 
NAL CAK GYY sing 181 n n 
CAK CAJ GYY sing 182 n n 
CAJ CAI GYY sing 183 n n 
CAI NAH GYY sing 184 n n 
NAH CAG GYY sing 185 n n 
CAG OAC GYY doub 186 n n 
CAG CAF GYY sing 187 n n 
CAF CAE GYY sing 188 n n 
CAE CAB GYY doub 189 n y 
CAE CAW GYY sing 190 n y 
CAB CAA GYY sing 191 n y 
CAY CAW GYY doub 192 n y 
CAY CBA GYY sing 193 n y 
CAW CAV GYY sing 194 n y 
CAA CAD GYY doub 195 n y 
CBA CAZ GYY doub 196 n y 
CAV CAD GYY sing 197 n y 
CAV CAX GYY doub 198 n y 
CAZ CAX GYY sing 199 n y 
CAA HAA1 GYY sing 200 n n 
CAB HAB1 GYY sing 201 n n 
CAD HAD1 GYY sing 202 n n 
CAF HAF1 GYY sing 203 n n 
CAF HAF2 GYY sing 204 n n 
CAI HAI1 GYY sing 205 n n 
CAI HAI2 GYY sing 206 n n 
CAJ HAJ2 GYY sing 207 n n 
CAJ HAJ1 GYY sing 208 n n 
CAK HAK1 GYY sing 209 n n 
CAK HAK2 GYY sing 210 n n 
CAM HAM2 GYY sing 211 n n 
CAM HAM1 GYY sing 212 n n 
CAN HAN2 GYY sing 213 n n 
CAN HAN1 GYY sing 214 n n 
CAO HAO2 GYY sing 215 n n 
CAO HAO1 GYY sing 216 n n 
CAP HAP1 GYY sing 217 n n 
CAP HAP2 GYY sing 218 n n 
CAR HAR1 GYY sing 219 n n 
CAR HAR2 GYY sing 220 n n 
CAS HAS2 GYY sing 221 n n 
CAS HAS1 GYY sing 222 n n 
CAT HAT2 GYY sing 223 n n 
CAT HAT1 GYY sing 224 n n 
CAX HAX1 GYY sing 225 n n 
CAY HAY1 GYY sing 226 n n 
CAZ HAZ1 GYY sing 227 n n 
CBA HBA1 GYY sing 228 n n 
NAH HAH1 GYY sing 229 n n 
NAL H1 GYY sing 230 n n 
NAQ H2 GYY sing 231 n n 
NAU H3 GYY sing 232 n n 
NAU HAU2 GYY sing 233 n n 
#
_atom_sites.entry_id                     6DM1 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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 GLU A 1 1301 1301 GLU GLU . 
F 3 CYZ A 1 1302 1302 CYZ CYZ . 
G 2 GLU B 1 1301 1301 GLU GLU . 
H 3 CYZ B 1 1302 1302 CYZ CYZ . 
I 2 GLU C 1 1301 1301 GLU GLU . 
J 3 CYZ C 1 1302 1302 CYZ CYZ . 
K 4 GYY C 1 1303 1 GYY DRG . 
L 2 GLU D 1 1301 1301 GLU GLU . 
M 3 CYZ D 1 1302 1302 CYZ CYZ . 
#
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 CAA GYY . . . K 4 164.298 160.376 113.438 1 119.01 ? CAA GYY 1303 C 1 
HETATM 2 C CAB GYY . . . K 4 164.106 160.911 112.165 1 119.01 ? CAB GYY 1303 C 1 
HETATM 3 C CAD GYY . . . K 4 163.518 160.797 114.5 1 119.01 ? CAD GYY 1303 C 1 
HETATM 4 C CAE GYY . . . K 4 163.123 161.869 111.958 1 119.01 ? CAE GYY 1303 C 1 
HETATM 5 C CAF GYY . . . K 4 162.956 162.421 110.545 1 119.01 ? CAF GYY 1303 C 1 
HETATM 6 C CAG GYY . . . K 4 161.684 161.955 109.824 1 119.01 ? CAG GYY 1303 C 1 
HETATM 7 C CAI GYY . . . K 4 162.707 162.033 107.492 1 119.01 ? CAI GYY 1303 C 1 
HETATM 8 C CAJ GYY . . . K 4 162.173 162.755 106.287 1 119.01 ? CAJ GYY 1303 C 1 
HETATM 9 C CAK GYY . . . K 4 161.532 161.813 105.317 1 119.01 ? CAK GYY 1303 C 1 
HETATM 10 C CAM GYY . . . K 4 161.544 162.081 102.976 1 119.01 ? CAM GYY 1303 C 1 
HETATM 11 C CAN GYY . . . K 4 162.404 162.128 101.715 1 119.01 ? CAN GYY 1303 C 1 
HETATM 12 C CAO GYY . . . K 4 161.618 161.862 100.429 1 119.01 ? CAO GYY 1303 C 1 
HETATM 13 C CAP GYY . . . K 4 162.49 161.902 99.18 1 119.01 ? CAP GYY 1303 C 1 
HETATM 14 C CAR GYY . . . K 4 162.485 161.706 96.828 1 119.01 ? CAR GYY 1303 C 1 
HETATM 15 C CAS GYY . . . K 4 161.743 162.039 95.532 1 119.01 ? CAS GYY 1303 C 1 
HETATM 16 C CAT GYY . . . K 4 162.436 161.506 94.275 1 119.01 ? CAT GYY 1303 C 1 
HETATM 17 C CAV GYY . . . K 4 162.515 161.781 114.291 1 119.01 ? CAV GYY 1303 C 1 
HETATM 18 C CAW GYY . . . K 4 162.32 162.311 113.05 1 119.01 ? CAW GYY 1303 C 1 
HETATM 19 C CAX GYY . . . K 4 161.718 162.209 115.385 1 119.01 ? CAX GYY 1303 C 1 
HETATM 20 C CAY GYY . . . K 4 161.312 163.299 112.86 1 119.01 ? CAY GYY 1303 C 1 
HETATM 21 C CAZ GYY . . . K 4 160.736 163.17 115.19 1 119.01 ? CAZ GYY 1303 C 1 
HETATM 22 C CBA GYY . . . K 4 160.533 163.711 113.928 1 119.01 ? CBA GYY 1303 C 1 
HETATM 23 N NAH GYY . . . K 4 161.604 161.786 108.382 1 119.01 ? NAH GYY 1303 C 1 
HETATM 24 N NAL GYY . . . K 4 162.359 161.813 104.14 1 119.01 ? NAL GYY 1303 C 1 
HETATM 25 N NAQ GYY . . . K 4 161.668 162.006 97.99 1 119.01 ? NAQ GYY 1303 C 1 
HETATM 26 N NAU GYY . . . K 4 163.501 162.407 93.87 1 119.01 ? NAU GYY 1303 C 1 
HETATM 27 O OAC GYY . . . K 4 160.711 161.719 110.449 1 119.01 ? OAC GYY 1303 C 1 
HETATM 28 H HAA1 GYY . . . K 4 164.951 159.737 113.58 1 119.01 ? HAA1 GYY 1303 C 1 
HETATM 29 H HAB1 GYY . . . K 4 164.632 160.627 111.452 1 119.01 ? HAB1 GYY 1303 C 1 
HETATM 30 H HAD1 GYY . . . K 4 163.653 160.435 115.345 1 119.01 ? HAD1 GYY 1303 C 1 
HETATM 31 H HAF1 GYY . . . K 4 162.963 163.391 110.571 1 119.01 ? HAF1 GYY 1303 C 1 
HETATM 32 H HAF2 GYY . . . K 4 163.726 162.117 110.046 1 119.01 ? HAF2 GYY 1303 C 1 
HETATM 33 H HAI1 GYY . . . K 4 163.36 162.602 107.894 1 119.01 ? HAI1 GYY 1303 C 1 
HETATM 34 H HAI2 GYY . . . K 4 163.111 161.199 107.231 1 119.01 ? HAI2 GYY 1303 C 1 
HETATM 35 H HAJ2 GYY . . . K 4 161.522 163.4 106.577 1 119.01 ? HAJ2 GYY 1303 C 1 
HETATM 36 H HAJ1 GYY . . . K 4 162.905 163.182 105.834 1 119.01 ? HAJ1 GYY 1303 C 1 
HETATM 37 H HAK1 GYY . . . K 4 161.49 160.933 105.7 1 119.01 ? HAK1 GYY 1303 C 1 
HETATM 38 H HAK2 GYY . . . K 4 160.645 162.121 105.123 1 119.01 ? HAK2 GYY 1303 C 1 
HETATM 39 H HAM2 GYY . . . K 4 160.883 161.377 102.896 1 119.01 ? HAM2 GYY 1303 C 1 
HETATM 40 H HAM1 GYY . . . K 4 161.104 162.937 103.083 1 119.01 ? HAM1 GYY 1303 C 1 
HETATM 41 H HAN2 GYY . . . K 4 162.812 163.008 101.653 1 119.01 ? HAN2 GYY 1303 C 1 
HETATM 42 H HAN1 GYY . . . K 4 163.101 161.46 101.797 1 119.01 ? HAN1 GYY 1303 C 1 
HETATM 43 H HAO2 GYY . . . K 4 161.209 160.984 100.487 1 119.01 ? HAO2 GYY 1303 C 1 
HETATM 44 H HAO1 GYY . . . K 4 160.926 162.534 100.335 1 119.01 ? HAO1 GYY 1303 C 1 
HETATM 45 H HAP1 GYY . . . K 4 163.073 162.672 99.227 1 119.01 ? HAP1 GYY 1303 C 1 
HETATM 46 H HAP2 GYY . . . K 4 163.021 161.092 99.134 1 119.01 ? HAP2 GYY 1303 C 1 
HETATM 47 H HAR1 GYY . . . K 4 163.299 162.226 96.873 1 119.01 ? HAR1 GYY 1303 C 1 
HETATM 48 H HAR2 GYY . . . K 4 162.711 160.765 96.836 1 119.01 ? HAR2 GYY 1303 C 1 
HETATM 49 H HAS2 GYY . . . K 4 160.853 161.662 95.579 1 119.01 ? HAS2 GYY 1303 C 1 
HETATM 50 H HAS1 GYY . . . K 4 161.669 163.002 95.456 1 119.01 ? HAS1 GYY 1303 C 1 
HETATM 51 H HAT2 GYY . . . K 4 162.805 160.627 94.45 1 119.01 ? HAT2 GYY 1303 C 1 
HETATM 52 H HAT1 GYY . . . K 4 161.788 161.44 93.557 1 119.01 ? HAT1 GYY 1303 C 1 
HETATM 53 H HAX1 GYY . . . K 4 161.856 161.847 116.229 1 119.01 ? HAX1 GYY 1303 C 1 
HETATM 54 H HAY1 GYY . . . K 4 161.169 163.66 112.016 1 119.01 ? HAY1 GYY 1303 C 1 
HETATM 55 H HAZ1 GYY . . . K 4 160.211 163.456 115.899 1 119.01 ? HAZ1 GYY 1303 C 1 
HETATM 56 H HBA1 GYY . . . K 4 159.877 164.35 113.802 1 119.01 ? HBA1 GYY 1303 C 1 
HETATM 57 H HAH1 GYY . . . K 4 160.866 161.528 108.035 1 119.01 ? HAH1 GYY 1303 C 1 
HETATM 58 H H1 GYY . . . K 4 162.738 161.016 104.065 1 119.01 ? H1 GYY 1303 C 1 
HETATM 59 H H2 GYY . . . K 4 161.352 162.835 97.926 1 119.01 ? H2 GYY 1303 C 1 
HETATM 60 H H3 GYY . . . K 4 163.813 162.159 93.074 1 119.01 ? H3 GYY 1303 C 1 
HETATM 61 H HAU2 GYY . . . K 4 163.184 163.236 93.819 1 119.01 ? HAU2 GYY 1303 C 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    48 
_model_server_stats.query_time_ms           229 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           61 
#