data_8SZF # _model_server_result.job_id yfwIWM5pPfEjCkNNSB6HPg _model_server_result.datetime_utc '2024-11-26 12:05:40' _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 8szf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":1008}' # _entry.id 8SZF # _exptl.entry_id 8SZF _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 202.34 _entity.id 9 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SPERMINE _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 8SZF _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8SZF _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,N,O,P,Q,R,S,T,U _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 9 _struct_asym.id U _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n C NAG 1 C 1 NAG A 904 NAG 3 n C NAG 2 C 2 NAG A 905 NAG 3 n D NAG 1 D 1 NAG A 906 NAG 3 n D NAG 2 D 2 NAG A 907 NAG 3 n E NAG 1 E 1 NAG B 905 NAG 3 n E NAG 2 E 2 NAG B 906 NAG # 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 52 A CYS 60 1_555 A SG CYS 93 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 228 A CYS 236 1_555 A SG CYS 553 A CYS 561 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 350 A CYS 358 1_555 A SG CYS 387 A CYS 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf4 A SG CYS 429 A CYS 437 1_555 A SG CYS 441 A CYS 449 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 534 A CYS 542 1_555 A SG CYS 554 A CYS 562 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf6 A SG CYS 538 A CYS 546 1_555 A SG CYS 557 A CYS 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf7 A SG CYS 560 A CYS 568 1_555 A SG CYS 574 A CYS 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 A SG CYS 577 A CYS 585 1_555 A SG CYS 590 A CYS 598 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf9 A SG CYS 669 A CYS 677 1_555 A SG CYS 757 A CYS 765 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf10 B SG CYS 74 B CYS 60 1_555 B SG CYS 115 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf11 B SG CYS 250 B CYS 236 1_555 B SG CYS 575 B CYS 561 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf12 B SG CYS 372 B CYS 358 1_555 B SG CYS 409 B CYS 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf13 B SG CYS 451 B CYS 437 1_555 B SG CYS 463 B CYS 449 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf14 B SG CYS 556 B CYS 542 1_555 B SG CYS 576 B CYS 562 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf15 B SG CYS 560 B CYS 546 1_555 B SG CYS 579 B CYS 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf16 B SG CYS 582 B CYS 568 1_555 B SG CYS 596 B CYS 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf17 B SG CYS 599 B CYS 585 1_555 B SG CYS 612 B CYS 598 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf18 B SG CYS 691 B CYS 677 1_555 B SG CYS 779 B CYS 765 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 253 A ASN 261 1_555 F C1 NAG . A NAG 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale2 A ND2 ASN 460 A ASN 468 1_555 G C1 NAG . A NAG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 A ND2 ASN 480 A ASN 488 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale4 A ND2 ASN 533 A ASN 541 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 B ND2 ASN 275 B ASN 261 1_555 T C1 NAG . B NAG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale6 B ND2 ASN 482 B ASN 468 1_555 O C1 NAG . B NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale7 B ND2 ASN 502 B ASN 488 1_555 N C1 NAG . B NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale8 B ND2 ASN 555 B ASN 541 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale9 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale10 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale11 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? metalc ? metalc1 A O SER 76 A SER 84 1_555 I CA CA . A CA 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.918 ? metalc ? metalc2 A O LEU 79 A LEU 87 1_555 I CA CA . A CA 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? metalc ? metalc3 A O LEU 80 A LEU 88 1_555 I CA CA . A CA 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.741 ? metalc ? metalc4 A OD1 ASP 226 A ASP 234 1_555 K CA CA . A CA 1206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc5 A O GLY 549 A GLY 557 1_555 J CA CA . A CA 1205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc6 K CA CA . A CA 1206 1_555 B O GLY 571 B GLY 557 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.078 ? metalc ? metalc7 B O SER 98 B SER 84 1_555 Q CA CA . B CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.53 ? metalc ? metalc8 B O LEU 102 B LEU 88 1_555 Q CA CA . B CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.992 ? # _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 322 n n N1 HN11 SPM sing 323 n n N1 HN12 SPM sing 324 n n C2 C3 SPM sing 325 n n C2 H21 SPM sing 326 n n C2 H22 SPM sing 327 n n C3 C4 SPM sing 328 n n C3 H31 SPM sing 329 n n C3 H32 SPM sing 330 n n C4 N5 SPM sing 331 n n C4 H41 SPM sing 332 n n C4 H42 SPM sing 333 n n N5 C6 SPM sing 334 n n N5 HN5 SPM sing 335 n n C6 C7 SPM sing 336 n n C6 H61 SPM sing 337 n n C6 H62 SPM sing 338 n n C7 C8 SPM sing 339 n n C7 H71 SPM sing 340 n n C7 H72 SPM sing 341 n n C8 C9 SPM sing 342 n n C8 H81 SPM sing 343 n n C8 H82 SPM sing 344 n n C9 N10 SPM sing 345 n n C9 H91 SPM sing 346 n n C9 H92 SPM sing 347 n n N10 C11 SPM sing 348 n n N10 HN0 SPM sing 349 n n C11 C12 SPM sing 350 n n C11 H111 SPM sing 351 n n C11 H112 SPM sing 352 n n C12 C13 SPM sing 353 n n C12 H121 SPM sing 354 n n C12 H122 SPM sing 355 n n C13 N14 SPM sing 356 n n C13 H131 SPM sing 357 n n C13 H132 SPM sing 358 n n N14 HN41 SPM sing 359 n n N14 HN42 SPM sing 360 n n # _atom_sites.entry_id 8SZF _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 F 4 NAG A 1 1201 901 NAG NAG . G 4 NAG A 1 1202 903 NAG NAG . H 5 TRP A 1 1203 910 TRP TRP . I 6 CA A 1 1204 911 CA CA . J 6 CA A 1 1205 912 CA CA . K 6 CA A 1 1206 913 CA CA . L 7 PO4 A 1 1207 914 PO4 PO4 . M 8 YP4 A 1 1208 1001 YP4 YP4 . N 4 NAG B 1 1001 903 NAG NAG . O 4 NAG B 1 1002 904 NAG NAG . P 5 TRP B 1 1003 910 TRP TRP . Q 6 CA B 1 1004 911 CA CA . R 7 PO4 B 1 1005 912 PO4 PO4 . S 8 YP4 B 1 1006 1002 YP4 YP4 . T 4 NAG B 1 1007 1003 NAG NAG . U 9 SPM B 1 1008 1101 SPM SPM . # 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 . . . U 9 205.542 201.107 162.658 1 39.47 ? N1 SPM 1008 B 1 HETATM 2 C C2 SPM . . . U 9 205.415 201.051 164.107 1 40.53 ? C2 SPM 1008 B 1 HETATM 3 C C3 SPM . . . U 9 204.208 200.179 164.494 1 38.57 ? C3 SPM 1008 B 1 HETATM 4 C C4 SPM . . . U 9 203.867 200.316 165.989 1 37.42 ? C4 SPM 1008 B 1 HETATM 5 N N5 SPM . . . U 9 202.787 199.398 166.342 1 39.16 ? N5 SPM 1008 B 1 HETATM 6 C C6 SPM . . . U 9 202.592 199.346 167.788 1 39.36 ? C6 SPM 1008 B 1 HETATM 7 C C7 SPM . . . U 9 201.432 198.409 168.165 1 37.8 ? C7 SPM 1008 B 1 HETATM 8 C C8 SPM . . . U 9 200.855 198.785 169.542 1 37.02 ? C8 SPM 1008 B 1 HETATM 9 C C9 SPM . . . U 9 199.587 197.978 169.868 1 40.19 ? C9 SPM 1008 B 1 HETATM 10 N N10 SPM . . . U 9 198.782 198.68 170.866 1 41.83 ? N10 SPM 1008 B 1 HETATM 11 C C11 SPM . . . U 9 198.515 197.871 172.053 1 39.03 ? C11 SPM 1008 B 1 HETATM 12 C C12 SPM . . . U 9 199.719 197.924 173.008 1 38.4 ? C12 SPM 1008 B 1 HETATM 13 C C13 SPM . . . U 9 199.465 197.109 174.285 1 39.87 ? C13 SPM 1008 B 1 HETATM 14 N N14 SPM . . . U 9 200.56 197.322 175.219 1 37.86 ? N14 SPM 1008 B 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 46 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #