data_9GRO # _model_server_result.job_id 5LPP2W5s9Hq86Rs_fD9XfA _model_server_result.datetime_utc '2025-07-27 16:15:25' _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 9gro # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1203}' # _entry.id 9GRO # _exptl.entry_id 9GRO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 202.34 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SPERMINE _entity.pdbx_number_of_molecules 2 _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 9GRO _cell.length_a 114.586 _cell.length_b 114.586 _cell.length_c 172.179 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9GRO _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 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,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,GA 1 1 B,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,HA 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 ? 3 D N N ? 3 E 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 A SG CYS 260 A CYS 793 1_555 B SG CYS 260 B CYS 793 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc1 A NE2 HIS 118 A HIS 651 1_555 C ZN ZN . A ZN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc2 A OE2 GLU 263 A GLU 796 1_555 C ZN ZN . A ZN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.908 ? metalc ? metalc3 A ND1 HIS 303 A HIS 836 1_555 C ZN ZN . A ZN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc4 A ND1 HIS 464 A HIS 1064 1_555 C ZN ZN . A ZN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc5 B NE2 HIS 118 B HIS 651 1_555 U ZN ZN . B ZN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc6 B OE2 GLU 263 B GLU 796 1_555 U ZN ZN . B ZN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? metalc ? metalc7 B ND1 HIS 303 B HIS 836 1_555 U ZN ZN . B ZN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc8 B ND1 HIS 464 B HIS 1064 1_555 U ZN ZN . B ZN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? # _chem_comp.formula 'C10 H26 N4' _chem_comp.formula_weight 202.34 _chem_comp.id SPM _chem_comp.mon_nstd_flag . _chem_comp.name SPERMINE _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 N1 C2 SPM sing 422 n n N1 HN11 SPM sing 423 n n N1 HN12 SPM sing 424 n n C2 C3 SPM sing 425 n n C2 H21 SPM sing 426 n n C2 H22 SPM sing 427 n n C3 C4 SPM sing 428 n n C3 H31 SPM sing 429 n n C3 H32 SPM sing 430 n n C4 N5 SPM sing 431 n n C4 H41 SPM sing 432 n n C4 H42 SPM sing 433 n n N5 C6 SPM sing 434 n n N5 HN5 SPM sing 435 n n C6 C7 SPM sing 436 n n C6 H61 SPM sing 437 n n C6 H62 SPM sing 438 n n C7 C8 SPM sing 439 n n C7 H71 SPM sing 440 n n C7 H72 SPM sing 441 n n C8 C9 SPM sing 442 n n C8 H81 SPM sing 443 n n C8 H82 SPM sing 444 n n C9 N10 SPM sing 445 n n C9 H91 SPM sing 446 n n C9 H92 SPM sing 447 n n N10 C11 SPM sing 448 n n N10 HN0 SPM sing 449 n n C11 C12 SPM sing 450 n n C11 H111 SPM sing 451 n n C11 H112 SPM sing 452 n n C12 C13 SPM sing 453 n n C12 H121 SPM sing 454 n n C12 H122 SPM sing 455 n n C13 N14 SPM sing 456 n n C13 H131 SPM sing 457 n n C13 H132 SPM sing 458 n n N14 HN41 SPM sing 459 n n N14 HN42 SPM sing 460 n n # _atom_sites.entry_id 9GRO _atom_sites.fract_transf_matrix[1][1] 0.008727 _atom_sites.fract_transf_matrix[1][2] 0.005039 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010077 _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] 0.005808 _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 C 2 ZN A 1 1201 2000 ZN ZN . D 3 SPM A 1 1202 2001 SPM SPM . E 3 SPM A 1 1203 2002 SPM SPM . F 4 ORN A 1 1204 2003 ORN ORN . G 5 PUT A 1 1205 2004 PUT PUT . H 5 PUT A 1 1206 2005 PUT PUT . I 6 EDO A 1 1207 2006 EDO EDO . J 6 EDO A 1 1208 2007 EDO EDO . K 6 EDO A 1 1209 2008 EDO EDO . L 6 EDO A 1 1210 2009 EDO EDO . M 6 EDO A 1 1211 2010 EDO EDO . N 5 PUT A 1 1212 2011 PUT PUT . O 6 EDO A 1 1213 2012 EDO EDO . P 6 EDO A 1 1214 2013 EDO EDO . Q 7 I8P A 1 1215 3000 I8P I8P . R 6 EDO A 1 1216 3001 EDO EDO . S 6 EDO A 1 1217 3002 EDO EDO . T 5 PUT A 1 1218 3003 PUT PUT . U 2 ZN B 1 1201 2000 ZN ZN . V 8 1JW B 1 1202 2001 1JW 1JW . W 5 PUT B 1 1203 2002 PUT PUT . X 8 1JW B 1 1204 2003 1JW 1JW . Y 6 EDO B 1 1205 2004 EDO EDO . Z 6 EDO B 1 1206 2005 EDO EDO . AA 6 EDO B 1 1207 2006 EDO EDO . BA 5 PUT B 1 1208 2007 PUT PUT . CA 6 EDO B 1 1209 2008 EDO EDO . DA 7 I8P B 1 1210 3000 I8P I8P . EA 6 EDO B 1 1211 3001 EDO EDO . FA 6 EDO B 1 1212 3003 EDO EDO . GA 9 HOH A 1 1301 50 HOH HOH . GA 9 HOH A 2 1302 19 HOH HOH . GA 9 HOH A 3 1303 5 HOH HOH . GA 9 HOH A 4 1304 45 HOH HOH . GA 9 HOH A 5 1305 33 HOH HOH . GA 9 HOH A 6 1306 48 HOH HOH . GA 9 HOH A 7 1307 30 HOH HOH . GA 9 HOH A 8 1308 25 HOH HOH . GA 9 HOH A 9 1309 1 HOH HOH . GA 9 HOH A 10 1310 3 HOH HOH . GA 9 HOH A 11 1311 23 HOH HOH . GA 9 HOH A 12 1312 24 HOH HOH . GA 9 HOH A 13 1313 51 HOH HOH . GA 9 HOH A 14 1314 29 HOH HOH . GA 9 HOH A 15 1315 41 HOH HOH . GA 9 HOH A 16 1316 10 HOH HOH . GA 9 HOH A 17 1317 35 HOH HOH . GA 9 HOH A 18 1318 26 HOH HOH . GA 9 HOH A 19 1319 15 HOH HOH . GA 9 HOH A 20 1320 34 HOH HOH . GA 9 HOH A 21 1321 37 HOH HOH . GA 9 HOH A 22 1322 9 HOH HOH . GA 9 HOH A 23 1323 7 HOH HOH . GA 9 HOH A 24 1324 40 HOH HOH . GA 9 HOH A 25 1325 8 HOH HOH . GA 9 HOH A 26 1326 2 HOH HOH . GA 9 HOH A 27 1327 46 HOH HOH . HA 9 HOH B 1 1301 11 HOH HOH . HA 9 HOH B 2 1302 44 HOH HOH . HA 9 HOH B 3 1303 17 HOH HOH . HA 9 HOH B 4 1304 36 HOH HOH . HA 9 HOH B 5 1305 49 HOH HOH . HA 9 HOH B 6 1306 12 HOH HOH . HA 9 HOH B 7 1307 22 HOH HOH . HA 9 HOH B 8 1308 32 HOH HOH . HA 9 HOH B 9 1309 6 HOH HOH . HA 9 HOH B 10 1310 16 HOH HOH . HA 9 HOH B 11 1311 39 HOH HOH . HA 9 HOH B 12 1312 4 HOH HOH . HA 9 HOH B 13 1313 13 HOH HOH . HA 9 HOH B 14 1314 20 HOH HOH . HA 9 HOH B 15 1315 47 HOH HOH . HA 9 HOH B 16 1316 18 HOH HOH . HA 9 HOH B 17 1317 42 HOH HOH . HA 9 HOH B 18 1318 21 HOH HOH . HA 9 HOH B 19 1319 14 HOH HOH . HA 9 HOH B 20 1320 27 HOH HOH . HA 9 HOH B 21 1321 31 HOH HOH . HA 9 HOH B 22 1322 43 HOH HOH . HA 9 HOH B 23 1323 28 HOH HOH . HA 9 HOH B 24 1324 38 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 N N1 SPM . . . E 3 18.899 -15.061 11.362 1 94.91 ? N1 SPM 1203 A 1 HETATM 2 C C2 SPM . . . E 3 17.592 -15.442 11.863 1 100.68 ? C2 SPM 1203 A 1 HETATM 3 C C3 SPM . . . E 3 17.64 -16.859 12.431 1 106.18 ? C3 SPM 1203 A 1 HETATM 4 C C4 SPM . . . E 3 18.953 -17.081 13.174 1 111.56 ? C4 SPM 1203 A 1 HETATM 5 N N5 SPM . . . E 3 19.86 -17.809 12.305 1 108.92 ? N5 SPM 1203 A 1 HETATM 6 C C6 SPM . . . E 3 21.046 -18.164 13.056 1 106.17 ? C6 SPM 1203 A 1 HETATM 7 C C7 SPM . . . E 3 21.857 -19.211 12.297 1 100.11 ? C7 SPM 1203 A 1 HETATM 8 C C8 SPM . . . E 3 23.185 -19.358 13.032 1 94.58 ? C8 SPM 1203 A 1 HETATM 9 C C9 SPM . . . E 3 23.985 -20.535 12.484 1 95.61 ? C9 SPM 1203 A 1 HETATM 10 N N10 SPM . . . E 3 24.965 -20.922 13.487 1 103.04 ? N10 SPM 1203 A 1 HETATM 11 C C11 SPM . . . E 3 25.964 -21.817 12.926 1 93.54 ? C11 SPM 1203 A 1 HETATM 12 C C12 SPM . . . E 3 25.281 -23.085 12.419 1 99.55 ? C12 SPM 1203 A 1 HETATM 13 C C13 SPM . . . E 3 26.292 -24.22 12.266 1 102.33 ? C13 SPM 1203 A 1 HETATM 14 N N14 SPM . . . E 3 27.028 -24.073 11.024 1 86.69 ? N14 SPM 1203 A 1 HETATM 15 H HN11 SPM . . . E 3 18.816 -14.378 10.797 1 114.15 ? HN11 SPM 1203 A 1 HETATM 16 H HN12 SPM . . . E 3 19.284 -15.751 10.957 1 114.15 ? HN12 SPM 1203 A 1 HETATM 17 H H21 SPM . . . E 3 17.323 -14.825 12.561 1 121.07 ? H21 SPM 1203 A 1 HETATM 18 H H22 SPM . . . E 3 16.948 -15.409 11.137 1 121.07 ? H22 SPM 1203 A 1 HETATM 19 H H31 SPM . . . E 3 17.57 -17.498 11.705 1 127.67 ? H31 SPM 1203 A 1 HETATM 20 H H32 SPM . . . E 3 16.899 -16.984 13.044 1 127.67 ? H32 SPM 1203 A 1 HETATM 21 H H41 SPM . . . E 3 19.344 -16.225 13.41 1 134.13 ? H41 SPM 1203 A 1 HETATM 22 H H42 SPM . . . E 3 18.79 -17.595 13.98 1 134.13 ? H42 SPM 1203 A 1 HETATM 23 H H61 SPM . . . E 3 21.59 -17.373 13.189 1 127.66 ? H61 SPM 1203 A 1 HETATM 24 H H62 SPM . . . E 3 20.784 -18.525 13.917 1 127.66 ? H62 SPM 1203 A 1 HETATM 25 H H71 SPM . . . E 3 22.011 -18.917 11.385 1 120.39 ? H71 SPM 1203 A 1 HETATM 26 H H72 SPM . . . E 3 21.384 -20.058 12.288 1 120.39 ? H72 SPM 1203 A 1 HETATM 27 H H81 SPM . . . E 3 23.701 -18.545 12.921 1 113.75 ? H81 SPM 1203 A 1 HETATM 28 H H82 SPM . . . E 3 23.011 -19.505 13.975 1 113.75 ? H82 SPM 1203 A 1 HETATM 29 H H91 SPM . . . E 3 24.438 -20.274 11.666 1 114.98 ? H91 SPM 1203 A 1 HETATM 30 H H92 SPM . . . E 3 23.392 -21.28 12.3 1 114.98 ? H92 SPM 1203 A 1 HETATM 31 H H111 SPM . . . E 3 26.416 -21.376 12.19 1 112.5 ? H111 SPM 1203 A 1 HETATM 32 H H112 SPM . . . E 3 26.611 -22.049 13.611 1 112.5 ? H112 SPM 1203 A 1 HETATM 33 H H121 SPM . . . E 3 24.873 -22.904 11.558 1 119.71 ? H121 SPM 1203 A 1 HETATM 34 H H122 SPM . . . E 3 24.596 -23.353 13.052 1 119.71 ? H122 SPM 1203 A 1 HETATM 35 H H131 SPM . . . E 3 25.822 -25.068 12.262 1 123.05 ? H131 SPM 1203 A 1 HETATM 36 H H132 SPM . . . E 3 26.913 -24.198 13.011 1 123.05 ? H132 SPM 1203 A 1 HETATM 37 H HN41 SPM . . . E 3 27.735 -24.612 11.036 1 104.29 ? HN41 SPM 1203 A 1 HETATM 38 H HN42 SPM . . . E 3 26.505 -24.298 10.342 1 104.29 ? HN42 SPM 1203 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 56 _model_server_stats.query_time_ms 347 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 38 #