data_6Y4M # _model_server_result.job_id SdYYfAyjJv2E0wSKqrpU9Q _model_server_result.datetime_utc '2025-02-17 23:58:05' _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 6y4m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":1006}' # _entry.id 6Y4M # _exptl.entry_id 6Y4M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 207.269 _entity.id 12 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2~{S},4~{R})-4-azanyl-2-methyl-5-phenyl-pentanoic acid' _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 6Y4M _cell.length_a 103.961 _cell.length_b 152.59 _cell.length_c 185.989 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6Y4M _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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 12 _struct_asym.id O _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # 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 covale ? covale1 M C31 O9B . B O9B 1004 1_555 T N VAL . C VAL 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale2 N C5 O9H . B O9H 1005 1_555 O NBI OH5 . B OH5 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale3 N N3 O9H . B O9H 1005 1_555 T C VAL . C VAL 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.356 ? metalc ? metalc1 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.963 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.095 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc7 G O1G GTP . A GTP 1001 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc8 G O1B GTP . A GTP 1001 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc9 H MG MG . A MG 1002 1_555 X O HOH . A HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc10 H MG MG . A MG 1002 1_555 X O HOH . A HOH 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc11 H MG MG . A MG 1002 1_555 X O HOH . A HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc12 H MG MG . A MG 1002 1_555 X O HOH . A HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc13 K MG MG . B MG 1002 1_555 Y O HOH . B HOH 1109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? metalc ? metalc14 K MG MG . B MG 1002 1_555 Z O HOH . C HOH 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.818 ? metalc ? metalc15 C OD1 ASP 39 C ASP 39 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.783 ? metalc ? metalc16 C OD2 ASP 39 C ASP 39 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc17 C O THR 41 C THR 41 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc18 C OG1 THR 41 C THR 41 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc19 C O GLY 44 C GLY 44 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc20 C OE1 GLU 55 C GLU 55 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.006 ? metalc ? metalc21 C OE2 GLU 55 C GLU 55 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc22 P O1G GTP . C GTP 1001 1_555 Q MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? metalc ? metalc23 P O1B GTP . C GTP 1001 1_555 Q MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc24 Q MG MG . C MG 1002 1_555 Z O HOH . C HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc25 Q MG MG . C MG 1002 1_555 Z O HOH . C HOH 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc26 Q MG MG . C MG 1002 1_555 Z O HOH . C HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc27 Q MG MG . C MG 1002 1_555 Z O HOH . C HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc28 U O1G GTP . D GTP 1001 1_555 V MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.789 ? metalc ? metalc29 U O1B GTP . D GTP 1001 1_555 V MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? metalc ? metalc30 V MG MG . D MG 1002 1_555 AA O HOH . D HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc31 V MG MG . D MG 1002 1_555 AA O HOH . D HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc32 V MG MG . D MG 1002 1_555 AA O HOH . D HOH 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc33 V MG MG . D MG 1002 1_555 AA O HOH . D HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? # _chem_comp.formula 'C12 H17 N O2' _chem_comp.formula_weight 207.269 _chem_comp.id OH5 _chem_comp.mon_nstd_flag . _chem_comp.name '(2~{S},4~{R})-4-azanyl-2-methyl-5-phenyl-pentanoic acid' _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 CBL CBJ OH5 sing 494 n n CBL CBT OH5 sing 495 n n CBM CBJ OH5 sing 496 n n CBM CBN OH5 sing 497 n n NBI CBJ OH5 sing 498 n n CBT CBX OH5 sing 499 n n CBT CBU OH5 sing 500 n n CBS CBN OH5 doub 501 n y CBS CBR OH5 sing 502 n y CBN CBO OH5 sing 503 n y CBR CBQ OH5 doub 504 n y OXT CBU OH5 doub 505 n n CBU O OH5 sing 506 n n CBO CBP OH5 doub 507 n y CBQ CBP OH5 sing 508 n y NBI H1 OH5 sing 509 n n NBI H2 OH5 sing 510 n n CBJ H4 OH5 sing 511 n n CBL H5 OH5 sing 512 n n CBL H6 OH5 sing 513 n n CBT H7 OH5 sing 514 n n CBX H8 OH5 sing 515 n n CBX H9 OH5 sing 516 n n CBX H10 OH5 sing 517 n n O H11 OH5 sing 518 n n CBM H12 OH5 sing 519 n n CBM H13 OH5 sing 520 n n CBO H14 OH5 sing 521 n n CBP H15 OH5 sing 522 n n CBQ H16 OH5 sing 523 n n CBR H17 OH5 sing 524 n n CBS H18 OH5 sing 525 n n # _atom_sites.entry_id 6Y4M _atom_sites.fract_transf_matrix[1][1] 0.009619 _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] 0.006554 _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] 0.005377 _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 GTP A 1 1001 1001 GTP GTP . H 6 MG A 1 1002 1002 MG MO6 . I 7 CA A 1 1003 1003 CA CA . J 8 GDP B 1 1001 1001 GDP GDP . K 6 MG B 1 1002 1002 MG MG . L 9 MES B 1 1003 1004 MES MES . M 10 O9B B 1 1004 2001 O9B ABB . N 11 O9H B 1 1005 2001 O9H ABB . O 12 OH5 B 1 1006 2001 OH5 ABB . P 5 GTP C 1 1001 1001 GTP GTP . Q 6 MG C 1 1002 1002 MG MO6 . R 7 CA C 1 1003 1003 CA CA . S 13 PGE C 1 1004 1004 PGE PGE . T 14 VAL C 1 1005 2001 VAL ABB . U 5 GTP D 1 1001 1001 GTP GTP . V 6 MG D 1 1002 1002 MG MO6 . W 15 ACP F 1 401 401 ACP ACP . X 16 HOH A 1 1101 1002 HOH MO6 . X 16 HOH A 2 1102 1002 HOH MO6 . X 16 HOH A 3 1103 1002 HOH MO6 . X 16 HOH A 4 1104 11 HOH HOH . X 16 HOH A 5 1105 1002 HOH MO6 . X 16 HOH A 6 1106 8 HOH HOH . X 16 HOH A 7 1107 10 HOH HOH . X 16 HOH A 8 1108 13 HOH HOH . X 16 HOH A 9 1109 7 HOH HOH . Y 16 HOH B 1 1101 20 HOH HOH . Y 16 HOH B 2 1102 18 HOH HOH . Y 16 HOH B 3 1103 5 HOH HOH . Y 16 HOH B 4 1104 16 HOH HOH . Y 16 HOH B 5 1105 4 HOH HOH . Y 16 HOH B 6 1106 14 HOH HOH . Y 16 HOH B 7 1107 6 HOH HOH . Y 16 HOH B 8 1108 21 HOH HOH . Y 16 HOH B 9 1109 1 HOH HOH . Y 16 HOH B 10 1110 9 HOH HOH . Y 16 HOH B 11 1111 19 HOH HOH . Z 16 HOH C 1 1101 1002 HOH MO6 . Z 16 HOH C 2 1102 1002 HOH MO6 . Z 16 HOH C 3 1103 1002 HOH MO6 . Z 16 HOH C 4 1104 15 HOH HOH . Z 16 HOH C 5 1105 1002 HOH MO6 . Z 16 HOH C 6 1106 2 HOH HOH . Z 16 HOH C 7 1107 3 HOH HOH . AA 16 HOH D 1 1101 1002 HOH MO6 . AA 16 HOH D 2 1102 17 HOH HOH . AA 16 HOH D 3 1103 1002 HOH MO6 . AA 16 HOH D 4 1104 1002 HOH MO6 . AA 16 HOH D 5 1105 1002 HOH MO6 . BA 16 HOH E 1 201 12 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 NBI OH5 . . . O 12 -3.916 22.876 13.124 1 65.21 ? NBI OH5 1006 B 1 HETATM 2 C CBJ OH5 . . . O 12 -4.032 21.427 13.247 1 67.66 ? CBJ OH5 1006 B 1 HETATM 3 C CBL OH5 . . . O 12 -2.907 20.731 12.466 1 70.73 ? CBL OH5 1006 B 1 HETATM 4 C CBT OH5 . . . O 12 -1.932 19.927 13.339 1 73.01 ? CBT OH5 1006 B 1 HETATM 5 C CBX OH5 . . . O 12 -2.579 18.655 13.87 1 73.05 ? CBX OH5 1006 B 1 HETATM 6 C CBU OH5 . . . O 12 -1.367 20.787 14.477 1 74.57 ? CBU OH5 1006 B 1 HETATM 7 O O OH5 . . . O 12 -1.907 20.714 15.6 1 71.23 ? O OH5 1006 B 1 HETATM 8 O OXT OH5 . . . O 12 -0.388 21.515 14.227 1 80.04 ? OXT OH5 1006 B 1 HETATM 9 C CBM OH5 . . . O 12 -5.426 20.977 12.793 1 66.69 ? CBM OH5 1006 B 1 HETATM 10 C CBN OH5 . . . O 12 -6.54 21.569 13.627 1 67.33 ? CBN OH5 1006 B 1 HETATM 11 C CBO OH5 . . . O 12 -7.105 20.859 14.675 1 69.65 ? CBO OH5 1006 B 1 HETATM 12 C CBP OH5 . . . O 12 -8.118 21.417 15.441 1 69.75 ? CBP OH5 1006 B 1 HETATM 13 C CBQ OH5 . . . O 12 -8.576 22.687 15.169 1 69.3 ? CBQ OH5 1006 B 1 HETATM 14 C CBR OH5 . . . O 12 -8.023 23.403 14.138 1 67.6 ? CBR OH5 1006 B 1 HETATM 15 C CBS OH5 . . . O 12 -7.01 22.846 13.373 1 67.33 ? CBS OH5 1006 B 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 15 #