data_6IKM # _model_server_result.job_id lp3yTVgqdPBcVsYempkZLA _model_server_result.datetime_utc '2024-10-20 20:57:57' _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 6ikm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"XC","auth_seq_id":407}' # _entry.id 6IKM # _exptl.entry_id 6IKM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 145.246 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SPERMIDINE _entity.pdbx_number_of_molecules 18 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 120.08 _cell.angle_gamma 90 _cell.entry_id 6IKM _cell.length_a 146.235 _cell.length_b 481.804 _cell.length_c 146.134 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6IKM _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 ? dimeric 2 author_defined_assembly 3 ? dimeric 2 author_defined_assembly 4 ? dimeric 2 author_defined_assembly 5 ? dimeric 2 author_defined_assembly 6 ? dimeric 2 author_defined_assembly 7 ? dimeric 2 author_defined_assembly 8 ? dimeric 2 author_defined_assembly 9 ? dimeric 2 author_defined_assembly 10 ? dimeric 2 author_defined_assembly 11 ? dimeric 2 author_defined_assembly 12 ? dimeric 2 author_defined_assembly 13 ? dimeric 2 author_defined_assembly 14 ? dimeric 2 author_defined_assembly 15 ? dimeric 2 author_defined_assembly 16 ? dimeric 2 author_defined_assembly 17 ? dimeric 2 author_defined_assembly 18 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,KA,LA,MA,NA 1 1 C,D,OA,PA,QA,RA,SA 2 1 E,F,TA,UA,VA,WA 3 1 G,H,XA,YA,ZA,AB 4 1 I,J,BB,CB,DB,EB,FB 5 1 K,L,GB,HB,IB,JB 6 1 M,N,KB,LB,MB 7 1 O,P,NB,OB,PB 8 1 Q,R,QB,RB,SB,TB 9 1 S,T,UB,VB,WB,XB 10 1 U,V,YB,ZB,AC,BC 11 1 W,X,CC,DC,EC,FC 12 1 Y,Z,GC,HC,IC,JC 13 1 AA,BA,KC,LC,MC,NC,OC,PC,QC 14 1 CA,DA,RC,SC,TC,UC,VC,WC,XC 15 1 EA,FA,YC 16 1 GA,HA,ZC 17 1 IA,JA,AD,BD,CD,DD 18 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 NA N N ? 4 SA N N ? 4 WA N N ? 4 AB N N ? 4 FB N N ? 4 JB N N ? 4 MB N N ? 4 PB N N ? 4 TB N N ? 4 XB N N ? 4 BC N N ? 4 FC N N ? 4 JC N N ? 4 QC N N ? 4 XC N N ? 4 YC N N ? 4 ZC N N ? 4 DD 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 disulf ? disulf1 B SG CYS 24 a CYS 24 1_555 B SG CYS 98 a CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 B SG CYS 155 a CYS 155 1_555 B SG CYS 222 a CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 D SG CYS 24 b CYS 24 1_555 D SG CYS 98 b CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 D SG CYS 155 b CYS 155 1_555 D SG CYS 222 b CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf5 F SG CYS 24 c CYS 24 1_555 F SG CYS 98 c CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 F SG CYS 155 c CYS 155 1_555 F SG CYS 222 c CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf7 H SG CYS 24 d CYS 24 1_555 H SG CYS 98 d CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 H SG CYS 155 d CYS 155 1_555 H SG CYS 222 d CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf9 J SG CYS 24 e CYS 24 1_555 J SG CYS 98 e CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf10 J SG CYS 155 e CYS 155 1_555 J SG CYS 222 e CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf11 L SG CYS 24 f CYS 24 1_555 L SG CYS 98 f CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf12 L SG CYS 155 f CYS 155 1_555 L SG CYS 222 f CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf13 N SG CYS 24 g CYS 24 1_555 N SG CYS 98 g CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf14 N SG CYS 155 g CYS 155 1_555 N SG CYS 222 g CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf15 O SG CYS 149 H CYS 171 1_555 O SG CYS 212 H CYS 234 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf16 P SG CYS 24 h CYS 24 1_555 P SG CYS 98 h CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf17 P SG CYS 155 h CYS 155 1_555 P SG CYS 222 h CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf18 R SG CYS 24 i CYS 24 1_555 R SG CYS 98 i CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf19 R SG CYS 155 i CYS 155 1_555 R SG CYS 222 i CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf20 T SG CYS 24 j CYS 24 1_555 T SG CYS 98 j CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf21 T SG CYS 155 j CYS 155 1_555 T SG CYS 222 j CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf22 V SG CYS 24 k CYS 24 1_555 V SG CYS 98 k CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf23 V SG CYS 155 k CYS 155 1_555 V SG CYS 222 k CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf24 X SG CYS 24 l CYS 24 1_555 X SG CYS 98 l CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf25 X SG CYS 155 l CYS 155 1_555 X SG CYS 222 l CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf26 Z SG CYS 24 m CYS 24 1_555 Z SG CYS 98 m CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf27 Z SG CYS 155 m CYS 155 1_555 Z SG CYS 222 m CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf28 BA SG CYS 24 n CYS 24 1_555 BA SG CYS 98 n CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf29 BA SG CYS 155 n CYS 155 1_555 BA SG CYS 222 n CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? disulf ? disulf30 DA SG CYS 24 o CYS 24 1_555 DA SG CYS 98 o CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf31 DA SG CYS 155 o CYS 155 1_555 DA SG CYS 222 o CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf32 FA SG CYS 24 p CYS 24 1_555 FA SG CYS 98 p CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf33 FA SG CYS 155 p CYS 155 1_555 FA SG CYS 222 p CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf34 HA SG CYS 24 q CYS 24 1_555 HA SG CYS 98 q CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf35 HA SG CYS 155 q CYS 155 1_555 HA SG CYS 222 q CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf36 JA SG CYS 24 r CYS 24 1_555 JA SG CYS 98 r CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf37 JA SG CYS 155 r CYS 155 1_555 JA SG CYS 222 r CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? # _chem_comp.formula 'C7 H19 N3' _chem_comp.formula_weight 145.246 _chem_comp.id SPD _chem_comp.mon_nstd_flag . _chem_comp.name SPERMIDINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE;PA(34) # 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 N1 C2 SPD sing 292 n n N1 HN11 SPD sing 293 n n N1 HN12 SPD sing 294 n n C2 C3 SPD sing 295 n n C2 H21 SPD sing 296 n n C2 H22 SPD sing 297 n n C3 C4 SPD sing 298 n n C3 H31 SPD sing 299 n n C3 H32 SPD sing 300 n n C4 C5 SPD sing 301 n n C4 H41 SPD sing 302 n n C4 H42 SPD sing 303 n n C5 N6 SPD sing 304 n n C5 H51 SPD sing 305 n n C5 H52 SPD sing 306 n n N6 C7 SPD sing 307 n n N6 HN6 SPD sing 308 n n C7 C8 SPD sing 309 n n C7 H71 SPD sing 310 n n C7 H72 SPD sing 311 n n C8 C9 SPD sing 312 n n C8 H81 SPD sing 313 n n C8 H82 SPD sing 314 n n C9 N10 SPD sing 315 n n C9 H91 SPD sing 316 n n C9 H92 SPD sing 317 n n N10 H101 SPD sing 318 n n N10 H102 SPD sing 319 n n # _atom_sites.entry_id 6IKM _atom_sites.fract_transf_matrix[1][1] 0.006838 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003961 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.002076 _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] 0.007908 _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 KA 3 SO4 A 1 401 368 SO4 SO4 . LA 3 SO4 A 1 402 369 SO4 SO4 . MA 3 SO4 A 1 403 371 SO4 SO4 . NA 4 SPD A 1 404 383 SPD SPD . OA 3 SO4 B 1 401 368 SO4 SO4 . PA 3 SO4 B 1 402 369 SO4 SO4 . QA 3 SO4 B 1 403 370 SO4 SO4 . RA 3 SO4 B 1 404 371 SO4 SO4 . SA 4 SPD B 1 405 383 SPD SPD . TA 3 SO4 C 1 401 368 SO4 SO4 . UA 3 SO4 C 1 402 369 SO4 SO4 . VA 3 SO4 C 1 403 371 SO4 SO4 . WA 4 SPD C 1 404 383 SPD SPD . XA 3 SO4 D 1 401 368 SO4 SO4 . YA 3 SO4 D 1 402 369 SO4 SO4 . ZA 3 SO4 D 1 403 371 SO4 SO4 . AB 4 SPD D 1 404 383 SPD SPD . BB 3 SO4 E 1 401 368 SO4 SO4 . CB 3 SO4 E 1 402 369 SO4 SO4 . DB 3 SO4 E 1 403 370 SO4 SO4 . EB 3 SO4 E 1 404 371 SO4 SO4 . FB 4 SPD E 1 405 383 SPD SPD . GB 3 SO4 F 1 401 368 SO4 SO4 . HB 3 SO4 F 1 402 369 SO4 SO4 . IB 3 SO4 F 1 403 371 SO4 SO4 . JB 4 SPD F 1 404 383 SPD SPD . KB 3 SO4 G 1 401 366 SO4 SO4 . LB 3 SO4 G 1 402 367 SO4 SO4 . MB 4 SPD G 1 403 383 SPD SPD . NB 3 SO4 H 1 401 366 SO4 SO4 . OB 3 SO4 H 1 402 367 SO4 SO4 . PB 4 SPD H 1 403 383 SPD SPD . QB 3 SO4 I 1 401 366 SO4 SO4 . RB 3 SO4 I 1 402 367 SO4 SO4 . SB 3 SO4 I 1 403 370 SO4 SO4 . TB 4 SPD I 1 404 383 SPD SPD . UB 3 SO4 J 1 401 366 SO4 SO4 . VB 3 SO4 J 1 402 367 SO4 SO4 . WB 3 SO4 J 1 403 370 SO4 SO4 . XB 4 SPD J 1 404 383 SPD SPD . YB 3 SO4 K 1 401 366 SO4 SO4 . ZB 3 SO4 K 1 402 367 SO4 SO4 . AC 3 SO4 K 1 403 370 SO4 SO4 . BC 4 SPD K 1 404 383 SPD SPD . CC 3 SO4 L 1 401 368 SO4 SO4 . DC 3 SO4 L 1 402 369 SO4 SO4 . EC 3 SO4 L 1 403 371 SO4 SO4 . FC 4 SPD L 1 404 383 SPD SPD . GC 3 SO4 M 1 401 366 SO4 SO4 . HC 3 SO4 M 1 402 367 SO4 SO4 . IC 3 SO4 M 1 403 370 SO4 SO4 . JC 4 SPD M 1 404 383 SPD SPD . KC 3 SO4 N 1 401 366 SO4 SO4 . LC 3 SO4 N 1 402 367 SO4 SO4 . MC 3 SO4 N 1 403 368 SO4 SO4 . NC 3 SO4 N 1 404 369 SO4 SO4 . OC 3 SO4 N 1 405 370 SO4 SO4 . PC 3 SO4 N 1 406 371 SO4 SO4 . QC 4 SPD N 1 407 383 SPD SPD . RC 3 SO4 O 1 401 366 SO4 SO4 . SC 3 SO4 O 1 402 367 SO4 SO4 . TC 3 SO4 O 1 403 368 SO4 SO4 . UC 3 SO4 O 1 404 369 SO4 SO4 . VC 3 SO4 O 1 405 370 SO4 SO4 . WC 3 SO4 O 1 406 371 SO4 SO4 . XC 4 SPD O 1 407 383 SPD SPD . YC 4 SPD P 1 401 383 SPD SPD . ZC 4 SPD Q 1 401 383 SPD SPD . AD 3 SO4 R 1 401 366 SO4 SO4 . BD 3 SO4 R 1 402 367 SO4 SO4 . CD 3 SO4 R 1 403 370 SO4 SO4 . DD 4 SPD R 1 404 383 SPD SPD . # 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 N N1 SPD . . . XC 4 -8.681 -241.407 60.332 1 67.7 ? N1 SPD 407 O 1 HETATM 2 C C2 SPD . . . XC 4 -9.13 -240.119 59.886 1 67.54 ? C2 SPD 407 O 1 HETATM 3 C C3 SPD . . . XC 4 -8.74 -239.93 58.425 1 67.55 ? C3 SPD 407 O 1 HETATM 4 C C4 SPD . . . XC 4 -9.652 -240.765 57.532 1 67.51 ? C4 SPD 407 O 1 HETATM 5 C C5 SPD . . . XC 4 -9.349 -240.398 56.075 1 67.49 ? C5 SPD 407 O 1 HETATM 6 N N6 SPD . . . XC 4 -9.097 -241.609 55.323 1 67.57 ? N6 SPD 407 O 1 HETATM 7 C C7 SPD . . . XC 4 -8.808 -241.296 53.942 1 67.56 ? C7 SPD 407 O 1 HETATM 8 C C8 SPD . . . XC 4 -8.168 -242.54 53.321 1 67.69 ? C8 SPD 407 O 1 HETATM 9 C C9 SPD . . . XC 4 -7.105 -242.187 52.289 1 67.66 ? C9 SPD 407 O 1 HETATM 10 N N10 SPD . . . XC 4 -5.895 -242.903 52.589 1 67.77 ? N10 SPD 407 O 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 35 _model_server_stats.create_model_time_ms 88 _model_server_stats.query_time_ms 606 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 10 #