data_6KBQ # _model_server_result.job_id va2QHaU78rGq0I0ayYhmiw _model_server_result.datetime_utc '2024-11-25 12:54:14' _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 6kbq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":410}' # _entry.id 6KBQ # _exptl.entry_id 6KBQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 4 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 120 _cell.entry_id 6KBQ _cell.length_a 152.445 _cell.length_b 152.445 _cell.length_c 145.762 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KBQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 ? 4 G N N ? 4 H N N ? 4 I N N ? 4 J 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 B NAG 1 B 1 NAG A 374 NAG 2 n B NAG 2 B 2 NAG A 375 NAG 2 n C NAG 1 C 1 NAG A 376 NAG 2 n C NAG 2 C 2 NAG A 377 NAG 2 n D NAG 1 D 1 NAG A 378 NAG 2 n D NAG 2 D 2 NAG A 379 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 36 A CYS 36 1_555 A SG CYS 86 A CYS 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf2 A SG CYS 89 A CYS 89 1_555 A SG CYS 251 A CYS 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? disulf ? disulf3 A SG CYS 245 A CYS 245 1_555 A SG CYS 245 A CYS 245 7_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? covale ? covale1 A ND2 ASN 78 A ASN 78 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale2 A ND2 ASN 298 A ASN 298 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale3 A ND2 ASN 321 A ASN 321 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale4 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.472 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale6 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? metalc ? metalc1 A OD1 ASP 97 A ASP 97 1_555 F CA CA . A CA 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc2 A OD2 ASP 98 A ASP 98 1_555 F CA CA . A CA 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc3 A OD1 ASN 138 A ASN 138 1_555 F CA CA . A CA 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc4 A OG SER 143 A SER 143 1_555 F CA CA . A CA 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.571 ? metalc ? metalc5 A O PRO 144 A PRO 144 1_555 F CA CA . A CA 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc6 A OD1 ASP 259 A ASP 259 1_555 E CA CA . A CA 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.813 ? metalc ? metalc7 A OD2 ASP 260 A ASP 260 1_555 E CA CA . A CA 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? metalc ? metalc8 A OD1 ASN 301 A ASN 301 1_555 E CA CA . A CA 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.758 ? metalc ? metalc9 A O GLY 303 A GLY 303 1_555 E CA CA . A CA 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.727 ? metalc ? metalc10 A O PRO 305 A PRO 305 1_555 E CA CA . A CA 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.512 ? metalc ? metalc11 E CA CA . A CA 407 1_555 H O1 GOL . A GOL 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.971 ? metalc ? metalc12 E CA CA . A CA 407 1_555 H O2 GOL . A GOL 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.615 ? metalc ? metalc13 F CA CA . A CA 408 1_555 G O3 GOL . A GOL 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.673 ? metalc ? metalc14 F CA CA . A CA 408 1_555 G O2 GOL . A GOL 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? # _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 129 n n C1 C2 GOL sing 130 n n C1 H11 GOL sing 131 n n C1 H12 GOL sing 132 n n O1 HO1 GOL sing 133 n n C2 O2 GOL sing 134 n n C2 C3 GOL sing 135 n n C2 H2 GOL sing 136 n n O2 HO2 GOL sing 137 n n C3 O3 GOL sing 138 n n C3 H31 GOL sing 139 n n C3 H32 GOL sing 140 n n O3 HO3 GOL sing 141 n n # _atom_sites.entry_id 6KBQ _atom_sites.fract_transf_matrix[1][1] 0.00656 _atom_sites.fract_transf_matrix[1][2] 0.003787 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007575 _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] 0.00686 _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 E 3 CA A 1 407 1 CA CA . F 3 CA A 1 408 2 CA CA . G 4 GOL A 1 409 380 GOL GOL . H 4 GOL A 1 410 381 GOL GOL . I 4 GOL A 1 411 382 GOL GOL . J 4 GOL A 1 412 383 GOL GOL . K 5 HOH A 1 501 13 HOH HOH . K 5 HOH A 2 502 29 HOH HOH . K 5 HOH A 3 503 9 HOH HOH . K 5 HOH A 4 504 18 HOH HOH . K 5 HOH A 5 505 19 HOH HOH . K 5 HOH A 6 506 1 HOH HOH . K 5 HOH A 7 507 50 HOH HOH . K 5 HOH A 8 508 32 HOH HOH . K 5 HOH A 9 509 58 HOH HOH . K 5 HOH A 10 510 33 HOH HOH . K 5 HOH A 11 511 70 HOH HOH . K 5 HOH A 12 512 52 HOH HOH . K 5 HOH A 13 513 31 HOH HOH . K 5 HOH A 14 514 35 HOH HOH . K 5 HOH A 15 515 23 HOH HOH . K 5 HOH A 16 516 48 HOH HOH . K 5 HOH A 17 517 5 HOH HOH . K 5 HOH A 18 518 71 HOH HOH . K 5 HOH A 19 519 39 HOH HOH . K 5 HOH A 20 520 68 HOH HOH . K 5 HOH A 21 521 3 HOH HOH . K 5 HOH A 22 522 37 HOH HOH . K 5 HOH A 23 523 40 HOH HOH . K 5 HOH A 24 524 11 HOH HOH . K 5 HOH A 25 525 41 HOH HOH . K 5 HOH A 26 526 20 HOH HOH . K 5 HOH A 27 527 63 HOH HOH . K 5 HOH A 28 528 59 HOH HOH . K 5 HOH A 29 529 54 HOH HOH . K 5 HOH A 30 530 57 HOH HOH . K 5 HOH A 31 531 62 HOH HOH . K 5 HOH A 32 532 38 HOH HOH . K 5 HOH A 33 533 75 HOH HOH . K 5 HOH A 34 534 65 HOH HOH . K 5 HOH A 35 535 30 HOH HOH . K 5 HOH A 36 536 55 HOH HOH . K 5 HOH A 37 537 14 HOH HOH . K 5 HOH A 38 538 46 HOH HOH . K 5 HOH A 39 539 43 HOH HOH . K 5 HOH A 40 540 72 HOH HOH . K 5 HOH A 41 541 17 HOH HOH . K 5 HOH A 42 542 7 HOH HOH . K 5 HOH A 43 543 15 HOH HOH . K 5 HOH A 44 544 25 HOH HOH . K 5 HOH A 45 545 42 HOH HOH . K 5 HOH A 46 546 45 HOH HOH . K 5 HOH A 47 547 12 HOH HOH . K 5 HOH A 48 548 10 HOH HOH . K 5 HOH A 49 549 24 HOH HOH . K 5 HOH A 50 550 28 HOH HOH . K 5 HOH A 51 551 22 HOH HOH . K 5 HOH A 52 552 49 HOH HOH . K 5 HOH A 53 553 21 HOH HOH . K 5 HOH A 54 554 69 HOH HOH . K 5 HOH A 55 555 27 HOH HOH . K 5 HOH A 56 556 34 HOH HOH . K 5 HOH A 57 557 26 HOH HOH . K 5 HOH A 58 558 60 HOH HOH . K 5 HOH A 59 559 47 HOH HOH . K 5 HOH A 60 560 53 HOH HOH . K 5 HOH A 61 561 44 HOH HOH . K 5 HOH A 62 562 16 HOH HOH . K 5 HOH A 63 563 6 HOH HOH . K 5 HOH A 64 564 76 HOH HOH . K 5 HOH A 65 565 61 HOH HOH . K 5 HOH A 66 566 51 HOH HOH . K 5 HOH A 67 567 66 HOH HOH . K 5 HOH A 68 568 2 HOH HOH . K 5 HOH A 69 569 4 HOH HOH . K 5 HOH A 70 570 8 HOH HOH . K 5 HOH A 71 571 73 HOH HOH . K 5 HOH A 72 572 78 HOH HOH . K 5 HOH A 73 573 67 HOH HOH . K 5 HOH A 74 574 56 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 . . . H 4 63.924 64.618 72.381 1 57.55 ? C1 GOL 410 A 1 HETATM 2 O O1 GOL . . . H 4 62.585 64.338 71.919 1 49.62 ? O1 GOL 410 A 1 HETATM 3 C C2 GOL . . . H 4 64.243 66.187 72.416 1 56.36 ? C2 GOL 410 A 1 HETATM 4 O O2 GOL . . . H 4 63.385 66.882 73.231 1 55.12 ? O2 GOL 410 A 1 HETATM 5 C C3 GOL . . . H 4 65.714 66.315 72.905 1 59.19 ? C3 GOL 410 A 1 HETATM 6 O O3 GOL . . . H 4 66.491 65.564 72.006 1 68.98 ? O3 GOL 410 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 6 #