data_4PV1 # _model_server_result.job_id 2dIKSWkfr_I6mxJVRlo0zQ _model_server_result.datetime_utc '2024-11-06 03:18:48' _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 4pv1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":309}' # _entry.id 4PV1 # _exptl.entry_id 4PV1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 564.732 _entity.id 14 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate' _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 120 _cell.entry_id 4PV1 _cell.length_a 159.085 _cell.length_b 159.085 _cell.length_c 361.322 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PV1 _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 hexadecameric _pdbx_struct_assembly.oligomeric_count 16 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 12_565 x,x-y+1,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -79.5425 137.771651 60.220333 # _struct_asym.details ? _struct_asym.entity_id 14 _struct_asym.id Q _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 disulf ? disulf1 D SG CYS 113 D CYS 113 1_555 D SG CYS 128 D CYS 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? covale ? covale1 C SG CYS 25 C CYS 25 1_555 W CAC HEC . C HEC 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.814 ? metalc ? metalc1 A NE2 HIS 86 A HIS 86 1_555 K FE HEC . A HEC 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc2 A NE2 HIS 100 A HIS 100 1_555 L FE HEC . A HEC 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc3 A NE2 HIS 187 A HIS 187 1_555 K FE HEC . A HEC 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc4 A NE2 HIS 202 A HIS 202 1_555 L FE HEC . A HEC 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc5 M FE HEC . A HEC 305 1_555 P O8 SMA . A SMA 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc6 M FE HEC . A HEC 305 1_555 CA O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc7 U MG CLA . B CLA 204 1_555 DA O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc8 C N TYR 1 C TYR 1 1_555 W FE HEC . C HEC 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc9 C NE2 HIS 26 C HIS 26 1_555 W FE HEC . C HEC 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc10 D SG CYS 108 D CYS 108 1_555 X FE1 FES . D FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc11 D ND1 HIS 110 D HIS 110 1_555 X FE2 FES . D FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc12 D SG CYS 126 D CYS 126 1_555 X FE1 FES . D FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc13 D ND1 HIS 129 D HIS 129 1_555 X FE2 FES . D FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? # _chem_comp.formula 'C29 H57 O8 P' _chem_comp.formula_weight 564.732 _chem_comp.id 7PH _chem_comp.mon_nstd_flag . _chem_comp.name '(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'PHOSPHATIDIC ACID' # 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 O11 P 7PH sing 1 n n O14 P 7PH doub 2 n n P O13 7PH sing 3 n n P O12 7PH sing 4 n n O12 HO12 7PH sing 5 n n O13 HO13 7PH sing 6 n n C1 O11 7PH sing 7 n n C2 C1 7PH sing 8 n n C1 H1 7PH sing 9 n n C1 H1A 7PH sing 10 n n C3 C2 7PH sing 11 n n C2 O21 7PH sing 12 n n C2 H2 7PH sing 13 n n O31 C3 7PH sing 14 n n C3 H3 7PH sing 15 n n C3 H3A 7PH sing 16 n n C31 O31 7PH sing 17 n n C31 O32 7PH doub 18 n n C32 C31 7PH sing 19 n n C33 C32 7PH sing 20 n n C32 H32 7PH sing 21 n n C32 H32A 7PH sing 22 n n C33 C34 7PH sing 23 n n C33 H33 7PH sing 24 n n C33 H33A 7PH sing 25 n n C34 C35 7PH sing 26 n n C34 H34 7PH sing 27 n n C34 H34A 7PH sing 28 n n C35 C36 7PH sing 29 n n C35 H35 7PH sing 30 n n C35 H35A 7PH sing 31 n n C36 C37 7PH sing 32 n n C36 H36 7PH sing 33 n n C36 H36A 7PH sing 34 n n C37 C38 7PH sing 35 n n C37 H37 7PH sing 36 n n C37 H37A 7PH sing 37 n n C38 C39 7PH sing 38 n n C38 H38 7PH sing 39 n n C38 H38A 7PH sing 40 n n C39 C3A 7PH sing 41 n n C39 H39 7PH sing 42 n n C39 H39A 7PH sing 43 n n C3A C3B 7PH sing 44 n n C3A H3AA 7PH sing 45 n n C3A H3AB 7PH sing 46 n n C3B C3C 7PH sing 47 n n C3B H3B 7PH sing 48 n n C3B H3BA 7PH sing 49 n n C3C H3C 7PH sing 50 n n C3C H3CA 7PH sing 51 n n C3C H3CB 7PH sing 52 n n C21 O21 7PH sing 53 n n O22 C21 7PH doub 54 n n C21 C22 7PH sing 55 n n C23 C22 7PH sing 56 n n C22 H22 7PH sing 57 n n C22 H22A 7PH sing 58 n n C24 C23 7PH sing 59 n n C23 H23 7PH sing 60 n n C23 H23A 7PH sing 61 n n C25 C24 7PH sing 62 n n C24 H24 7PH sing 63 n n C24 H24A 7PH sing 64 n n C26 C25 7PH sing 65 n n C25 H25 7PH sing 66 n n C25 H25A 7PH sing 67 n n C27 C26 7PH sing 68 n n C26 H26 7PH sing 69 n n C26 H26A 7PH sing 70 n n C27 C28 7PH sing 71 n n C27 H27 7PH sing 72 n n C27 H27A 7PH sing 73 n n C28 C29 7PH sing 74 n n C28 H28 7PH sing 75 n n C28 H28A 7PH sing 76 n n C29 C2A 7PH sing 77 n n C29 H29 7PH sing 78 n n C29 H29A 7PH sing 79 n n C2A C2B 7PH sing 80 n n C2A H2A 7PH sing 81 n n C2A H2AA 7PH sing 82 n n C2B C2C 7PH sing 83 n n C2B H2B 7PH sing 84 n n C2B H2BA 7PH sing 85 n n C2C C2D 7PH sing 86 n n C2C H2C 7PH sing 87 n n C2C H2CA 7PH sing 88 n n C2D C2E 7PH sing 89 n n C2D H2D 7PH sing 90 n n C2D H2DA 7PH sing 91 n n C2E H2E 7PH sing 92 n n C2E H2EA 7PH sing 93 n n C2E H2EB 7PH sing 94 n n # _atom_sites.entry_id 4PV1 _atom_sites.fract_transf_matrix[1][1] 0.006286 _atom_sites.fract_transf_matrix[1][2] 0.003629 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007258 _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] 0.002768 _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 I 9 MYS A 1 301 301 MYS MYS . J 10 CD A 1 302 302 CD CD . K 11 HEC A 1 303 303 HEC HEM . L 11 HEC A 1 304 304 HEC HEM . M 11 HEC A 1 305 305 HEC HEM . N 12 UMQ A 1 306 306 UMQ UMQ . O 12 UMQ A 1 307 307 UMQ UMQ . P 13 SMA A 1 308 308 SMA SMA . Q 14 7PH A 1 309 309 7PH 7PH . R 15 8K6 B 1 201 201 8K6 8K6 . S 10 CD B 1 202 202 CD CD . T 12 UMQ B 1 203 203 UMQ UMQ . U 16 CLA B 1 204 204 CLA CLA . V 17 OPC B 1 205 205 OPC OPC . W 11 HEC C 1 301 301 HEC HEM . X 18 FES D 1 201 201 FES FES . Y 19 SQD D 1 202 202 SQD SQD . Z 17 OPC D 1 203 203 OPC OPC . AA 17 OPC E 1 101 101 OPC OPC . BA 20 BCR G 1 101 101 BCR BCR . CA 21 HOH A 1 401 401 HOH HOH . CA 21 HOH A 2 402 402 HOH HOH . CA 21 HOH A 3 403 403 HOH HOH . CA 21 HOH A 4 404 404 HOH HOH . CA 21 HOH A 5 405 405 HOH HOH . CA 21 HOH A 6 406 406 HOH HOH . CA 21 HOH A 7 407 407 HOH HOH . CA 21 HOH A 8 408 408 HOH HOH . DA 21 HOH B 1 301 301 HOH HOH . DA 21 HOH B 2 302 302 HOH HOH . DA 21 HOH B 3 303 303 HOH HOH . DA 21 HOH B 4 304 304 HOH HOH . DA 21 HOH B 5 305 305 HOH HOH . EA 21 HOH C 1 1101 1101 HOH HOH . EA 21 HOH C 2 1102 1102 HOH HOH . FA 21 HOH G 1 201 201 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 O O11 7PH . . . Q 14 -67.889 80.859 16.4 1 109.36 ? O11 7PH 309 A 1 HETATM 2 C C1 7PH . . . Q 14 -66.482 80.86 16.516 1 116.16 ? C1 7PH 309 A 1 HETATM 3 C C2 7PH . . . Q 14 -65.934 82.174 16.015 0 110.35 ? C2 7PH 309 A 1 HETATM 4 C C3 7PH . . . Q 14 -65.431 83.008 17.186 1 104.73 ? C3 7PH 309 A 1 HETATM 5 O O31 7PH . . . Q 14 -65.269 84.378 16.753 0.75 109.35 ? O31 7PH 309 A 1 HETATM 6 O O32 7PH . . . Q 14 -63.661 85.04 18.293 1 99.53 ? O32 7PH 309 A 1 HETATM 7 C C31 7PH . . . Q 14 -63.986 84.96 17.111 0 105.32 ? C31 7PH 309 A 1 HETATM 8 C C32 7PH . . . Q 14 -62.919 85.18 16.003 1 87.16 ? C32 7PH 309 A 1 HETATM 9 C C33 7PH . . . Q 14 -62.277 86.578 16.147 1 94.14 ? C33 7PH 309 A 1 HETATM 10 C C34 7PH . . . Q 14 -61.193 86.761 15.07 1 90.92 ? C34 7PH 309 A 1 HETATM 11 C C35 7PH . . . Q 14 -59.797 86.494 15.683 1 89.14 ? C35 7PH 309 A 1 HETATM 12 C C36 7PH . . . Q 14 -58.7 86.777 14.631 1 86.3 ? C36 7PH 309 A 1 HETATM 13 C C37 7PH . . . Q 14 -57.347 86.853 15.311 1 73.24 ? C37 7PH 309 A 1 HETATM 14 C C38 7PH . . . Q 14 -56.244 87.121 14.263 1 65.55 ? C38 7PH 309 A 1 HETATM 15 C C39 7PH . . . Q 14 -56.116 88.622 14.008 1 78.84 ? C39 7PH 309 A 1 HETATM 16 C C3A 7PH . . . Q 14 -55.472 88.863 12.629 1 82.59 ? C3A 7PH 309 A 1 HETATM 17 C C3B 7PH . . . Q 14 -55.106 90.378 12.474 1 53.75 ? C3B 7PH 309 A 1 HETATM 18 O O21 7PH . . . Q 14 -64.858 81.933 15.127 0 112.39 ? O21 7PH 309 A 1 HETATM 19 O O22 7PH . . . Q 14 -66.159 82.9 13.486 1 107.5 ? O22 7PH 309 A 1 HETATM 20 C C21 7PH . . . Q 14 -65.123 82.342 13.758 1 115.86 ? C21 7PH 309 A 1 HETATM 21 C C22 7PH . . . Q 14 -64.003 82.264 12.713 1 108.51 ? C22 7PH 309 A 1 HETATM 22 C C23 7PH . . . Q 14 -62.626 82.385 13.419 1 79.08 ? C23 7PH 309 A 1 HETATM 23 C C24 7PH . . . Q 14 -61.552 82.739 12.379 1 77.49 ? C24 7PH 309 A 1 HETATM 24 C C25 7PH . . . Q 14 -60.16 82.562 12.989 1 85.32 ? C25 7PH 309 A 1 HETATM 25 C C26 7PH . . . Q 14 -59.1 82.793 11.893 1 83.07 ? C26 7PH 309 A 1 HETATM 26 C C27 7PH . . . Q 14 -57.677 82.828 12.521 1 70.29 ? C27 7PH 309 A 1 HETATM 27 C C28 7PH . . . Q 14 -56.646 82.967 11.396 1 67.32 ? C28 7PH 309 A 1 HETATM 28 C C29 7PH . . . Q 14 -55.218 82.837 11.973 1 73.75 ? C29 7PH 309 A 1 HETATM 29 C C2A 7PH . . . Q 14 -54.867 84.097 12.772 1 70.75 ? C2A 7PH 309 A 1 HETATM 30 C C2B 7PH . . . Q 14 -53.461 83.925 13.42 1 84.39 ? C2B 7PH 309 A 1 HETATM 31 C C2C 7PH . . . Q 14 -53.564 82.981 14.653 1 66.48 ? C2C 7PH 309 A 1 HETATM 32 C C2D 7PH . . . Q 14 -52.15 82.679 15.194 1 71.85 ? C2D 7PH 309 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 32 #