data_9I5P # _model_server_result.job_id Z4WP0XWmhVhjAz5AdTvIfQ _model_server_result.datetime_utc '2025-08-24 11:50:11' _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 9i5p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":604}' # _entry.id 9I5P # _exptl.entry_id 9I5P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 9I5P _cell.length_a 154.08 _cell.length_b 154.08 _cell.length_c 127.253 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9I5P _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall 'I 4 2' _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 8 _struct_asym.id J _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide 4 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 FUC NAG C1 O1 . O6 HO6 . sing 2 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 3 4 1 FUC NAG C1 O1 . O6 HO6 . sing 5 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . 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 B NAG 1 B 1 NAG A 530 NAG 2 n B FUC 2 B 2 FUC A 531 FUC 2 n C NAG 1 C 1 NAG A 532 NAG 2 n C FUC 2 C 2 FUC A 533 FUC 2 n D NAG 1 D 1 NAG A 534 NAG 2 n D FUC 2 D 2 FUC A 535 FUC 3 n E NAG 1 E 1 NAG A 537 NAG 3 n E NAG 2 E 2 NAG A 538 NAG 3 n E BMA 3 E 3 BMA A 539 BMA 3 n E FUC 4 E 4 FUC A 540 FUC 4 n F NAG 1 F 1 NAG A 541 NAG 4 n F NAG 2 F 2 NAG A 542 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 65 A CYS 65 1_555 A SG CYS 92 A CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf2 A SG CYS 252 A CYS 252 1_555 A SG CYS 263 A CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf3 A SG CYS 400 A CYS 400 1_555 A SG CYS 519 A CYS 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 57 A ASN 57 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale2 A ND2 ASN 106 A ASN 106 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.47 ? covale ? covale3 A ND2 ASN 241 A ASN 241 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale4 A ND2 ASN 256 A ASN 256 1_555 G C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale5 A ND2 ASN 341 A ASN 341 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale6 A ND2 ASN 485 A ASN 485 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale7 B O6 NAG . B NAG 1 1_555 B C1 FUC . B FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale8 C O6 NAG . C NAG 1 1_555 C C1 FUC . C FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? covale ? covale9 D O6 NAG . D NAG 1 1_555 D C1 FUC . D FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale10 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale11 E O6 NAG . E NAG 1 1_555 E C1 FUC . E FUC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale12 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale13 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 C1 O1 GOL sing 236 n n C1 C2 GOL sing 237 n n C1 H11 GOL sing 238 n n C1 H12 GOL sing 239 n n O1 HO1 GOL sing 240 n n C2 O2 GOL sing 241 n n C2 C3 GOL sing 242 n n C2 H2 GOL sing 243 n n O2 HO2 GOL sing 244 n n C3 O3 GOL sing 245 n n C3 H31 GOL sing 246 n n C3 H32 GOL sing 247 n n O3 HO3 GOL sing 248 n n # _atom_sites.entry_id 9I5P _atom_sites.fract_transf_matrix[1][1] 0.00649 _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] 0.00649 _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] 0.007858 _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 G 5 NAG A 1 601 536 NAG NAG . H 6 A1A2O A 1 602 543 A1A2O OF7 . I 7 SIA A 1 603 544 SIA SIA . J 8 GOL A 1 604 545 GOL GOL . K 9 MES A 1 605 546 MES MES . L 10 SO4 A 1 606 1 SO4 SO4 . M 10 SO4 A 1 607 2 SO4 SO4 . N 10 SO4 A 1 608 3 SO4 SO4 . O 11 HOH A 1 701 11 HOH HOH . O 11 HOH A 2 702 1 HOH HOH . O 11 HOH A 3 703 59 HOH HOH . O 11 HOH A 4 704 71 HOH HOH . O 11 HOH A 5 705 24 HOH HOH . O 11 HOH A 6 706 67 HOH HOH . O 11 HOH A 7 707 51 HOH HOH . O 11 HOH A 8 708 5 HOH HOH . O 11 HOH A 9 709 12 HOH HOH . O 11 HOH A 10 710 32 HOH HOH . O 11 HOH A 11 711 17 HOH HOH . O 11 HOH A 12 712 23 HOH HOH . O 11 HOH A 13 713 56 HOH HOH . O 11 HOH A 14 714 63 HOH HOH . O 11 HOH A 15 715 66 HOH HOH . O 11 HOH A 16 716 19 HOH HOH . O 11 HOH A 17 717 62 HOH HOH . O 11 HOH A 18 718 20 HOH HOH . O 11 HOH A 19 719 64 HOH HOH . O 11 HOH A 20 720 45 HOH HOH . O 11 HOH A 21 721 42 HOH HOH . O 11 HOH A 22 722 31 HOH HOH . O 11 HOH A 23 723 50 HOH HOH . O 11 HOH A 24 724 33 HOH HOH . O 11 HOH A 25 725 39 HOH HOH . O 11 HOH A 26 726 22 HOH HOH . O 11 HOH A 27 727 53 HOH HOH . O 11 HOH A 28 728 46 HOH HOH . O 11 HOH A 29 729 28 HOH HOH . O 11 HOH A 30 730 55 HOH HOH . O 11 HOH A 31 731 15 HOH HOH . O 11 HOH A 32 732 44 HOH HOH . O 11 HOH A 33 733 13 HOH HOH . O 11 HOH A 34 734 29 HOH HOH . O 11 HOH A 35 735 38 HOH HOH . O 11 HOH A 36 736 3 HOH HOH . O 11 HOH A 37 737 21 HOH HOH . O 11 HOH A 38 738 40 HOH HOH . O 11 HOH A 39 739 18 HOH HOH . O 11 HOH A 40 740 52 HOH HOH . O 11 HOH A 41 741 6 HOH HOH . O 11 HOH A 42 742 16 HOH HOH . O 11 HOH A 43 743 10 HOH HOH . O 11 HOH A 44 744 37 HOH HOH . O 11 HOH A 45 745 68 HOH HOH . O 11 HOH A 46 746 47 HOH HOH . O 11 HOH A 47 747 41 HOH HOH . O 11 HOH A 48 748 2 HOH HOH . O 11 HOH A 49 749 49 HOH HOH . O 11 HOH A 50 750 35 HOH HOH . O 11 HOH A 51 751 4 HOH HOH . O 11 HOH A 52 752 8 HOH HOH . O 11 HOH A 53 753 9 HOH HOH . O 11 HOH A 54 754 14 HOH HOH . O 11 HOH A 55 755 48 HOH HOH . O 11 HOH A 56 756 7 HOH HOH . O 11 HOH A 57 757 57 HOH HOH . O 11 HOH A 58 758 54 HOH HOH . O 11 HOH A 59 759 25 HOH HOH . O 11 HOH A 60 760 27 HOH HOH . O 11 HOH A 61 761 30 HOH HOH . O 11 HOH A 62 762 58 HOH HOH . O 11 HOH A 63 763 36 HOH HOH . O 11 HOH A 64 764 34 HOH HOH . O 11 HOH A 65 765 70 HOH HOH . O 11 HOH A 66 766 26 HOH HOH . O 11 HOH A 67 767 69 HOH HOH . O 11 HOH A 68 768 65 HOH HOH . O 11 HOH A 69 769 61 HOH HOH . O 11 HOH A 70 770 60 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 C C1 GOL . . . J 8 -5.798 -41.597 -22.484 1 80.09 ? C1 GOL 604 A 1 HETATM 2 O O1 GOL . . . J 8 -5.494 -41.146 -23.791 1 76.42 ? O1 GOL 604 A 1 HETATM 3 C C2 GOL . . . J 8 -6.773 -42.765 -22.509 1 81.17 ? C2 GOL 604 A 1 HETATM 4 O O2 GOL . . . J 8 -7.662 -42.724 -21.405 1 81.66 ? O2 GOL 604 A 1 HETATM 5 C C3 GOL . . . J 8 -6.05 -44.099 -22.575 1 82.95 ? C3 GOL 604 A 1 HETATM 6 O O3 GOL . . . J 8 -7.044 -45.092 -22.766 1 85.7 ? O3 GOL 604 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 350 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 6 #