data_8SZH # _model_server_result.job_id rpZ13q9dNTxZgXnNC8KJVA _model_server_result.datetime_utc '2024-10-18 05:23:08' _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 8szh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":909}' # _entry.id 8SZH # _exptl.entry_id 8SZH _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 202.34 _entity.id 12 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SPERMINE _entity.pdbx_number_of_molecules 4 _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 8SZH _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8SZH _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,V,W,X,Y,Z,AA,BA,CA _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 ? _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 ? 12 P N N ? 12 Q N N ? 12 AA N N ? 12 BA N N # _pdbx_entity_branch.entity_id 5 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 5 _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 5 n F NAG 1 F 1 NAG A 905 NAG 5 n F NAG 2 F 2 NAG A 906 NAG 5 n G NAG 1 G 1 NAG A 907 NAG 5 n G NAG 2 G 2 NAG A 908 NAG 5 n H NAG 1 H 1 NAG B 906 NAG 5 n H NAG 2 H 2 NAG B 907 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 429 A CYS 437 1_555 A SG CYS 441 A CYS 449 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 A SG CYS 534 A CYS 542 1_555 A SG CYS 554 A CYS 562 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 A SG CYS 538 A CYS 546 1_555 A SG CYS 557 A CYS 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 A SG CYS 560 A CYS 568 1_555 A SG CYS 574 A CYS 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 A SG CYS 577 A CYS 585 1_555 A SG CYS 590 A CYS 598 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 A SG CYS 669 A CYS 677 1_555 A SG CYS 757 A CYS 765 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf10 B SG CYS 52 B CYS 60 1_555 B SG CYS 93 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf11 B SG CYS 228 B CYS 236 1_555 B SG CYS 553 B CYS 561 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf12 B SG CYS 350 B CYS 358 1_555 B SG CYS 387 B CYS 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf13 B SG CYS 429 B CYS 437 1_555 B SG CYS 441 B CYS 449 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf14 B SG CYS 534 B CYS 542 1_555 B SG CYS 554 B CYS 562 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf15 B SG CYS 538 B CYS 546 1_555 B SG CYS 557 B CYS 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf16 B SG CYS 560 B CYS 568 1_555 B SG CYS 574 B CYS 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf17 B SG CYS 577 B CYS 585 1_555 B SG CYS 590 B CYS 598 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf18 B SG CYS 669 B CYS 677 1_555 B SG CYS 757 B CYS 765 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 A ND2 ASN 460 A ASN 468 1_555 K C1 NAG . A NAG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale2 A ND2 ASN 480 A ASN 488 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 A ND2 ASN 533 A ASN 541 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale4 B ND2 ASN 460 B ASN 468 1_555 U C1 NAG . B NAG 1404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 B ND2 ASN 480 B ASN 488 1_555 V C1 NAG . B NAG 1405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale6 B ND2 ASN 533 B ASN 541 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale7 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale8 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale9 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? metalc ? metalc1 A O ILE 73 A ILE 81 1_555 L CA CA . A CA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.17 ? metalc ? metalc2 A O SER 76 A SER 84 1_555 L CA CA . A CA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.959 ? metalc ? metalc3 A O LEU 79 A LEU 87 1_555 L CA CA . A CA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.778 ? metalc ? metalc4 A O LEU 80 A LEU 88 1_555 L CA CA . A CA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? metalc ? metalc5 A OD1 ASP 226 A ASP 234 1_555 M CA CA . A CA 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.866 ? metalc ? metalc6 M CA CA . A CA 905 1_555 B O GLY 549 B GLY 557 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? metalc ? metalc7 B O ASN 74 B ASN 82 1_555 W CA CA . B CA 1406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.16 ? metalc ? metalc8 B O LEU 80 B LEU 88 1_555 W CA CA . B CA 1406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.147 ? metalc ? metalc9 B O LEU 83 B LEU 91 1_555 W CA CA . B CA 1406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.809 ? # _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 539 n n N1 HN11 SPM sing 540 n n N1 HN12 SPM sing 541 n n C2 C3 SPM sing 542 n n C2 H21 SPM sing 543 n n C2 H22 SPM sing 544 n n C3 C4 SPM sing 545 n n C3 H31 SPM sing 546 n n C3 H32 SPM sing 547 n n C4 N5 SPM sing 548 n n C4 H41 SPM sing 549 n n C4 H42 SPM sing 550 n n N5 C6 SPM sing 551 n n N5 HN5 SPM sing 552 n n C6 C7 SPM sing 553 n n C6 H61 SPM sing 554 n n C6 H62 SPM sing 555 n n C7 C8 SPM sing 556 n n C7 H71 SPM sing 557 n n C7 H72 SPM sing 558 n n C8 C9 SPM sing 559 n n C8 H81 SPM sing 560 n n C8 H82 SPM sing 561 n n C9 N10 SPM sing 562 n n C9 H91 SPM sing 563 n n C9 H92 SPM sing 564 n n N10 C11 SPM sing 565 n n N10 HN0 SPM sing 566 n n C11 C12 SPM sing 567 n n C11 H111 SPM sing 568 n n C11 H112 SPM sing 569 n n C12 C13 SPM sing 570 n n C12 H121 SPM sing 571 n n C12 H122 SPM sing 572 n n C13 N14 SPM sing 573 n n C13 H131 SPM sing 574 n n C13 H132 SPM sing 575 n n N14 HN41 SPM sing 576 n n N14 HN42 SPM sing 577 n n # _atom_sites.entry_id 8SZH _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 I 6 YP4 A 1 901 900 YP4 YP4 . J 7 PCW A 1 902 901 PCW PCW . K 8 NAG A 1 903 904 NAG NAG . L 9 CA A 1 904 1001 CA CA . M 9 CA A 1 905 1002 CA CA . N 10 TRP A 1 906 1003 TRP TRP . O 11 PO4 A 1 907 1004 PO4 PO4 . P 12 SPM A 1 908 1301 SPM SPM . Q 12 SPM A 1 909 1401 SPM SPM . R 13 CLR B 1 1401 1401 CLR CLR . S 6 YP4 B 1 1402 900 YP4 YP4 . T 7 PCW B 1 1403 901 PCW PCW . U 8 NAG B 1 1404 904 NAG NAG . V 8 NAG B 1 1405 905 NAG NAG . W 9 CA B 1 1406 1001 CA CA . X 9 CA B 1 1407 1002 CA CA . Y 10 TRP B 1 1408 1003 TRP TRP . Z 11 PO4 B 1 1409 1004 PO4 PO4 . AA 12 SPM B 1 1410 1201 SPM SPM . BA 12 SPM B 1 1411 1301 SPM SPM . CA 14 HOH B 1 1501 1005 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 . . . Q 12 216.921 197.402 221.027 1 49.01 ? N1 SPM 909 A 1 HETATM 2 C C2 SPM . . . Q 12 216.97 198.053 222.324 1 51.74 ? C2 SPM 909 A 1 HETATM 3 C C3 SPM . . . Q 12 215.889 199.134 222.369 1 54.63 ? C3 SPM 909 A 1 HETATM 4 C C4 SPM . . . Q 12 216.222 200.263 223.363 1 52.91 ? C4 SPM 909 A 1 HETATM 5 N N5 SPM . . . Q 12 215.16 201.26 223.302 1 49.39 ? N5 SPM 909 A 1 HETATM 6 C C6 SPM . . . Q 12 213.934 200.558 222.957 1 52.7 ? C6 SPM 909 A 1 HETATM 7 C C7 SPM . . . Q 12 212.7 201.445 223.008 1 52.93 ? C7 SPM 909 A 1 HETATM 8 C C8 SPM . . . Q 12 211.469 200.551 223.167 1 52.75 ? C8 SPM 909 A 1 HETATM 9 C C9 SPM . . . Q 12 210.256 201.413 223.518 1 50.96 ? C9 SPM 909 A 1 HETATM 10 N N10 SPM . . . Q 12 209.052 200.634 223.261 1 54.61 ? N10 SPM 909 A 1 HETATM 11 C C11 SPM . . . Q 12 208.34 201.128 222.091 1 53.47 ? C11 SPM 909 A 1 HETATM 12 C C12 SPM . . . Q 12 208.296 202.664 222.167 1 54.54 ? C12 SPM 909 A 1 HETATM 13 C C13 SPM . . . Q 12 207.088 203.164 221.365 1 52.4 ? C13 SPM 909 A 1 HETATM 14 N N14 SPM . . . Q 12 205.91 202.911 222.166 1 48.11 ? N14 SPM 909 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #