data_6YMX # _model_server_result.job_id KAB44Notkldtrl1L7l97SA _model_server_result.datetime_utc '2024-12-27 03:24:15' _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 6ymx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"VA","auth_seq_id":401}' # _entry.id 6YMX # _exptl.entry_id 6YMX _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 592.785 _entity.id 33 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate' _entity.pdbx_number_of_molecules 2 _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 6YMX _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YMX _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 PISA _pdbx_struct_assembly.oligomeric_details 32-meric _pdbx_struct_assembly.oligomeric_count 32 _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,NB,OB,PB,QB,RB _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 ? 33 VA N N ? 33 NB N 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 disulf ? disulf1 J SG CYS 22 j CYS 27 1_555 J SG CYS 54 j CYS 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 J SG CYS 32 j CYS 37 1_555 J SG CYS 43 j CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 Q SG CYS 134 E CYS 164 1_555 Q SG CYS 150 E CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 R SG CYS 28 F CYS 101 1_555 R SG CYS 50 F CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 Z SG CYS 134 P CYS 164 1_555 Z SG CYS 150 P CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 AA SG CYS 29 Q CYS 101 1_555 AA SG CYS 51 Q CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 B N ILE 46 b ILE 61 1_555 MA C23 PTY . b PTY 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.287 ? covale ? covale2 B C ILE 46 b ILE 61 1_555 MA C23 PTY . b PTY 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.562 ? covale ? covale3 B CB ILE 46 b ILE 61 1_555 MA C23 PTY . b PTY 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.619 ? covale ? covale4 C CE MET 217 c MET 218 1_555 NA C36 PTY . c PTY 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? covale ? covale5 C CE MET 217 c MET 218 1_555 NA C37 PTY . c PTY 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? metalc ? metalc1 A NE2 HIS 58 a HIS 62 1_555 HA FE HEA . a HEA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc2 A ND1 HIS 237 a HIS 241 1_555 GA CU CU . a CU 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? metalc ? metalc3 A NE2 HIS 286 a HIS 290 1_555 GA CU CU . a CU 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc4 A NE2 HIS 287 a HIS 291 1_555 GA CU CU . a CU 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc5 A NE2 HIS 374 a HIS 378 1_555 HA FE HEA . a HEA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? metalc ? metalc6 B O GLU 208 b GLU 223 1_555 LA CU1 CUA . b CUA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc7 B ND1 HIS 214 b HIS 229 1_555 LA CU1 CUA . b CUA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc8 D SG CYS 105 d CYS 134 1_555 PA ZN ZN . d ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? metalc ? metalc9 O NE2 HIS 82 C HIS 82 1_555 WA FE HEM . C HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.668 ? metalc ? metalc10 O NE2 HIS 96 C HIS 96 1_555 XA FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? metalc ? metalc11 O NE2 HIS 183 C HIS 183 1_555 WA FE HEM . C HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc12 O NE2 HIS 197 C HIS 197 1_555 XA FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.746 ? metalc ? metalc13 P NE2 HIS 44 D HIS 105 1_555 CB FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? metalc ? metalc14 X NE2 HIS 82 N HIS 82 1_555 HB FE HEM . N HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.696 ? metalc ? metalc15 X NE2 HIS 96 N HIS 96 1_555 IB FE HEM . N HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? metalc ? metalc16 X NE2 HIS 183 N HIS 183 1_555 HB FE HEM . N HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.707 ? metalc ? metalc17 X NE2 HIS 197 N HIS 197 1_555 IB FE HEM . N HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.731 ? metalc ? metalc18 Y NE2 HIS 44 O HIS 105 1_555 OB FE HEM . O HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.673 ? # _chem_comp.formula 'C31 H61 O8 P' _chem_comp.formula_weight 592.785 _chem_comp.id 6PH _chem_comp.mon_nstd_flag . _chem_comp.name '(1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'PHOSPHATIDIC ACID' # _atom_sites.entry_id 6YMX _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 GA 26 CU a 1 601 601 CU CU . HA 27 HEA a 1 602 602 HEA HEA . IA 27 HEA a 1 603 603 HEA HEA . JA 28 PTY a 1 604 7 PTY PTY . KA 29 CN3 a 1 605 1 CN3 CN3 . LA 30 CUA b 1 301 301 CUA CUA . MA 28 PTY b 1 302 1 PTY PTY . NA 28 PTY c 1 301 6 PTY PTY . OA 31 PCF c 1 302 3 PCF PCF . PA 32 ZN d 1 201 1 ZN ZN . QA 31 PCF e 1 201 2 PCF PCF . RA 28 PTY i 1 101 3 PTY PTY . SA 28 PTY m 1 101 4 PTY PTY . TA 28 PTY m 1 102 5 PTY PTY . UA 31 PCF m 1 103 1 PCF PCF . VA 33 6PH C 1 401 401 6PH 6PH . WA 34 HEM C 1 402 402 HEM HEM . XA 34 HEM C 1 403 403 HEM HEM . YA 35 8PE C 1 404 404 8PE 8PE . ZA 36 CN5 C 1 405 405 CN5 CN5 . AB 37 UQ6 C 1 406 406 UQ6 UQ6 . BB 38 9PE C 1 407 401 9PE 9PE . CB 34 HEM D 1 401 401 HEM HEM . DB 28 PTY D 1 402 2 PTY PTY . EB 39 7PH E 1 301 402 7PH 7PH . FB 40 FES E 1 302 301 FES FES . GB 31 PCF I 1 101 101 PCF PCF . HB 34 HEM N 1 401 403 HEM HEM . IB 34 HEM N 1 402 404 HEM HEM . JB 37 UQ6 N 1 403 405 UQ6 UQ6 . KB 35 8PE N 1 404 406 8PE 8PE . LB 38 9PE N 1 405 407 9PE 9PE . MB 29 CN3 N 1 406 408 CN3 CN3 . NB 33 6PH O 1 401 402 6PH 6PH . OB 34 HEM O 1 402 401 HEM HEM . PB 39 7PH O 1 403 301 7PH 7PH . QB 40 FES P 1 301 302 FES FES . RB 31 PCF T 1 101 101 PCF PCF . # 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 P P 6PH . . . VA 33 199.646 189.296 199.816 1 70.67 ? P 6PH 401 C 1 HETATM 2 O O11 6PH . . . VA 33 199.628 190.892 199.709 1 70.67 ? O11 6PH 401 C 1 HETATM 3 O O12 6PH . . . VA 33 200.922 188.787 199.279 1 70.67 ? O12 6PH 401 C 1 HETATM 4 O O13 6PH . . . VA 33 199.519 188.88 201.357 1 70.67 ? O13 6PH 401 C 1 HETATM 5 O O14 6PH . . . VA 33 198.413 188.681 198.998 1 70.67 ? O14 6PH 401 C 1 HETATM 6 C C1 6PH . . . VA 33 200.536 191.682 200.466 1 70.67 ? C1 6PH 401 C 1 HETATM 7 C C2 6PH . . . VA 33 200.552 193.114 199.942 1 70.67 ? C2 6PH 401 C 1 HETATM 8 C C3 6PH . . . VA 33 200.992 193.1 198.482 1 70.67 ? C3 6PH 401 C 1 HETATM 9 O O31 6PH . . . VA 33 199.944 193.632 197.637 1 70.67 ? O31 6PH 401 C 1 HETATM 10 O O32 6PH . . . VA 33 201.44 194.29 196.168 1 70.67 ? O32 6PH 401 C 1 HETATM 11 C C31 6PH . . . VA 33 200.34 194.426 196.636 1 70.67 ? C31 6PH 401 C 1 HETATM 12 C C32 6PH . . . VA 33 199.425 195.495 196.101 1 70.67 ? C32 6PH 401 C 1 HETATM 13 C C33 6PH . . . VA 33 200.233 196.48 195.26 1 70.67 ? C33 6PH 401 C 1 HETATM 14 C C34 6PH . . . VA 33 200.244 197.838 195.954 1 70.67 ? C34 6PH 401 C 1 HETATM 15 C C35 6PH . . . VA 33 198.852 198.452 195.941 1 70.67 ? C35 6PH 401 C 1 HETATM 16 C C36 6PH . . . VA 33 199.01 199.944 196.199 1 70.67 ? C36 6PH 401 C 1 HETATM 17 C C37 6PH . . . VA 33 197.673 200.522 196.647 1 70.67 ? C37 6PH 401 C 1 HETATM 18 C C38 6PH . . . VA 33 197.899 201.943 197.16 1 70.67 ? C38 6PH 401 C 1 HETATM 19 C C39 6PH . . . VA 33 196.633 202.77 196.933 1 70.67 ? C39 6PH 401 C 1 HETATM 20 C C3A 6PH . . . VA 33 196.27 203.511 198.217 1 70.67 ? C3A 6PH 401 C 1 HETATM 21 C C3B 6PH . . . VA 33 194.782 203.856 198.185 1 70.67 ? C3B 6PH 401 C 1 HETATM 22 C C3C 6PH . . . VA 33 194.216 203.827 199.604 1 70.67 ? C3C 6PH 401 C 1 HETATM 23 C C3D 6PH . . . VA 33 194.889 204.902 200.457 1 70.67 ? C3D 6PH 401 C 1 HETATM 24 O O21 6PH . . . VA 33 199.223 193.674 200.044 1 70.67 ? O21 6PH 401 C 1 HETATM 25 O O22 6PH . . . VA 33 200.104 195.616 200.599 1 70.67 ? O22 6PH 401 C 1 HETATM 26 C C21 6PH . . . VA 33 199.119 194.975 200.34 1 70.67 ? C21 6PH 401 C 1 HETATM 27 C C22 6PH . . . VA 33 197.774 195.643 200.34 1 70.67 ? C22 6PH 401 C 1 HETATM 28 C C23 6PH . . . VA 33 197.95 197.154 200.469 1 70.67 ? C23 6PH 401 C 1 HETATM 29 C C24 6PH . . . VA 33 196.761 197.83 199.795 1 70.67 ? C24 6PH 401 C 1 HETATM 30 C C25 6PH . . . VA 33 196.199 198.929 200.693 1 70.67 ? C25 6PH 401 C 1 HETATM 31 C C26 6PH . . . VA 33 194.758 199.173 200.257 1 70.67 ? C26 6PH 401 C 1 HETATM 32 C C27 6PH . . . VA 33 193.92 199.73 201.4 1 70.67 ? C27 6PH 401 C 1 HETATM 33 C C28 6PH . . . VA 33 192.454 199.508 201.044 1 70.67 ? C28 6PH 401 C 1 HETATM 34 C C29 6PH . . . VA 33 191.564 200.34 201.962 1 70.67 ? C29 6PH 401 C 1 HETATM 35 C C2A 6PH . . . VA 33 191.874 201.827 201.785 1 70.67 ? C2A 6PH 401 C 1 HETATM 36 C C2B 6PH . . . VA 33 190.819 202.66 202.514 1 70.67 ? C2B 6PH 401 C 1 HETATM 37 C C2C 6PH . . . VA 33 191.5 203.805 203.26 1 70.67 ? C2C 6PH 401 C 1 HETATM 38 C C2D 6PH . . . VA 33 190.8 203.987 204.604 1 70.67 ? C2D 6PH 401 C 1 HETATM 39 C C2E 6PH . . . VA 33 191.403 205.178 205.348 1 70.67 ? C2E 6PH 401 C 1 HETATM 40 C C2F 6PH . . . VA 33 192.756 204.785 205.939 1 70.67 ? C2F 6PH 401 C 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 346 _model_server_stats.query_time_ms 470 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 40 #