data_9BU3 # _model_server_result.job_id S0gzP7XWSFap9pS7V7Q1ZQ _model_server_result.datetime_utc '2024-12-04 06:56:51' _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 9bu3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":502}' # _entry.id 9BU3 # _exptl.entry_id 9BU3 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 75.067 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCINE _entity.pdbx_number_of_molecules 5 _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 9BU3 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9BU3 _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_and_software_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,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 K N N ? 3 L N N ? 3 V N N ? 3 FA N N ? 3 PA N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _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 2 n F NAG 1 F 1 NAG A 502 NAG 2 n F NAG 2 F 2 NAG A 503 NAG 2 n G NAG 1 G 1 NAG B 502 NAG 2 n G NAG 2 G 2 NAG B 503 NAG 2 n H NAG 1 H 1 NAG C 502 NAG 2 n H NAG 2 H 2 NAG C 503 NAG 2 n I NAG 1 I 1 NAG D 502 NAG 2 n I NAG 2 I 2 NAG D 503 NAG 2 n J NAG 1 J 1 NAG E 502 NAG 2 n J NAG 2 J 2 NAG E 503 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 231 A CYS 198 1_555 A SG CYS 242 A CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 B SG CYS 231 B CYS 198 1_555 B SG CYS 242 B CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 C SG CYS 231 C CYS 198 1_555 C SG CYS 242 C CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 D SG CYS 231 D CYS 198 1_555 D SG CYS 242 D CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 E SG CYS 231 E CYS 198 1_555 E SG CYS 242 E CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 71 A ASN 38 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 B ND2 ASN 71 B ASN 38 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 C ND2 ASN 71 C ASN 38 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 D ND2 ASN 71 D ASN 38 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 E ND2 ASN 71 E ASN 38 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale6 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale7 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale8 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale9 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale10 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _chem_comp.formula 'C2 H5 N O2' _chem_comp.formula_weight 75.067 _chem_comp.id GLY _chem_comp.mon_nstd_flag y _chem_comp.name GLYCINE _chem_comp.type 'peptide linking' _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 N CA GLY sing 120 n n N H GLY sing 121 n n N H2 GLY sing 122 n n CA C GLY sing 123 n n CA HA2 GLY sing 124 n n CA HA3 GLY sing 125 n n C O GLY doub 126 n n C OXT GLY sing 127 n n OXT HXT GLY sing 128 n n # _atom_sites.entry_id 9BU3 _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 K 3 GLY A 1 501 501 GLY GLY . L 3 GLY A 1 502 501 GLY GLY . M 4 PIO A 1 503 504 PIO PIO . N 4 PIO A 1 504 506 PIO PIO . O 4 PIO A 1 505 507 PIO PIO . P 4 PIO A 1 506 508 PIO PIO . Q 5 PX4 A 1 507 509 PX4 PX4 . R 4 PIO A 1 508 505 PIO PIO . S 5 PX4 A 1 509 513 PX4 PX4 . T 5 PX4 A 1 510 514 PX4 PX4 . U 5 PX4 A 1 511 515 PX4 PX4 . V 3 GLY B 1 501 501 GLY GLY . W 4 PIO B 1 502 504 PIO PIO . X 4 PIO B 1 503 506 PIO PIO . Y 4 PIO B 1 504 507 PIO PIO . Z 4 PIO B 1 505 508 PIO PIO . AA 5 PX4 B 1 506 509 PX4 PX4 . BA 4 PIO B 1 507 505 PIO PIO . CA 5 PX4 B 1 508 513 PX4 PX4 . DA 5 PX4 B 1 509 514 PX4 PX4 . EA 5 PX4 B 1 510 515 PX4 PX4 . FA 3 GLY C 1 501 501 GLY GLY . GA 4 PIO C 1 502 504 PIO PIO . HA 4 PIO C 1 503 506 PIO PIO . IA 4 PIO C 1 504 507 PIO PIO . JA 4 PIO C 1 505 508 PIO PIO . KA 5 PX4 C 1 506 509 PX4 PX4 . LA 4 PIO C 1 507 505 PIO PIO . MA 5 PX4 C 1 508 513 PX4 PX4 . NA 5 PX4 C 1 509 514 PX4 PX4 . OA 5 PX4 C 1 510 515 PX4 PX4 . PA 3 GLY D 1 501 501 GLY GLY . QA 4 PIO D 1 502 504 PIO PIO . RA 4 PIO D 1 503 506 PIO PIO . SA 4 PIO D 1 504 507 PIO PIO . TA 4 PIO D 1 505 508 PIO PIO . UA 5 PX4 D 1 506 509 PX4 PX4 . VA 4 PIO D 1 507 505 PIO PIO . WA 5 PX4 D 1 508 513 PX4 PX4 . XA 5 PX4 D 1 509 514 PX4 PX4 . YA 5 PX4 D 1 510 515 PX4 PX4 . ZA 4 PIO E 1 501 505 PIO PIO . AB 5 PX4 E 1 502 513 PX4 PX4 . BB 5 PX4 E 1 503 514 PX4 PX4 . CB 5 PX4 E 1 504 515 PX4 PX4 . DB 4 PIO E 1 505 504 PIO PIO . EB 4 PIO E 1 506 506 PIO PIO . FB 4 PIO E 1 507 507 PIO PIO . GB 4 PIO E 1 508 508 PIO PIO . HB 5 PX4 E 1 509 509 PX4 PX4 . IB 6 HOH A 1 601 504 HOH HOH . IB 6 HOH A 2 602 505 HOH HOH . IB 6 HOH A 3 603 506 HOH HOH . JB 6 HOH B 1 601 504 HOH HOH . JB 6 HOH B 2 602 506 HOH HOH . JB 6 HOH B 3 603 505 HOH HOH . KB 6 HOH C 1 601 504 HOH HOH . KB 6 HOH C 2 602 505 HOH HOH . KB 6 HOH C 3 603 506 HOH HOH . LB 6 HOH D 1 601 504 HOH HOH . LB 6 HOH D 2 602 506 HOH HOH . LB 6 HOH D 3 603 505 HOH HOH . MB 6 HOH E 1 601 504 HOH HOH . MB 6 HOH E 2 602 506 HOH HOH . MB 6 HOH E 3 603 505 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 N GLY . . . L 3 164.267 139.633 197.311 1 71.48 ? N GLY 502 A 1 HETATM 2 C CA GLY . . . L 3 165.581 139.362 196.759 1 71.48 ? CA GLY 502 A 1 HETATM 3 C C GLY . . . L 3 166.64 139.136 197.819 1 71.48 ? C GLY 502 A 1 HETATM 4 O O GLY . . . L 3 166.351 139.148 199.015 1 71.48 ? O GLY 502 A 1 HETATM 5 O OXT GLY . . . L 3 167.814 138.935 197.51 1 71.48 ? OXT GLY 502 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 34 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 433 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 5 #