data_8C88 # _model_server_result.job_id -DXoHUsvTaoQZDEmmms24g _model_server_result.datetime_utc '2024-11-24 08:09:23' _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 8c88 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 8C88 # _exptl.entry_id 8C88 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 436.52 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate' _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 8C88 _cell.length_a 100.91 _cell.length_b 100.91 _cell.length_c 237.02 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8C88 _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall 'P 4n 2n' _symmetry.space_group_name_H-M 'P 42 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 D N N ? 4 T 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 B SG CYS 214 L CYS 214 1_555 C SG CYS 19 M CYS 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc1 B NE2 HIS 190 L HIS 190 1_555 X FE FE . M FE 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc2 B NE2 HIS 230 L HIS 230 1_555 X FE FE . M FE 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc3 C NE2 HIS 219 M HIS 219 1_555 X FE FE . M FE 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc4 C OE1 GLU 234 M GLU 234 1_555 X FE FE . M FE 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.564 ? metalc ? metalc5 C OE2 GLU 234 M GLU 234 1_555 X FE FE . M FE 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc6 C NE2 HIS 266 M HIS 266 1_555 X FE FE . M FE 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? # _chem_comp.formula 'C21 H41 O7 P' _chem_comp.formula_weight 436.52 _chem_comp.id NKP _chem_comp.mon_nstd_flag . _chem_comp.name '(2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '18:1 LPA;oleoyl lysophosphatidic 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 OAA PAC NKP sing 600 n n OAB PAC NKP sing 601 n n PAC OAD NKP doub 602 n n PAC OAF NKP sing 603 n n OAE CAK NKP doub 604 n n OAF CAG NKP sing 605 n n CAG CAH NKP sing 606 n n CAH CAI NKP sing 607 n n CAH OBC NKP sing 608 n n CAI OAJ NKP sing 609 n n OAJ CAK NKP sing 610 n n CAK CAL NKP sing 611 n n CAL CAM NKP sing 612 n n CAM CAN NKP sing 613 n n CAN CAO NKP sing 614 n n CAO CAP NKP sing 615 n n CAP CAQ NKP sing 616 n n CAQ CAR NKP sing 617 n n CAR CAS NKP sing 618 n n CAS CAT NKP doub 619 n n CAT CAU NKP sing 620 n n CAU CAV NKP sing 621 n n CAV CAW NKP sing 622 n n CAW CAX NKP sing 623 n n CAX CAY NKP sing 624 n n CAY CAZ NKP sing 625 n n CAZ CBA NKP sing 626 n n CBA CBB NKP sing 627 n n CAG HAG NKP sing 628 n n CAG HAGA NKP sing 629 n n CAH HAH NKP sing 630 n n CAI HAI NKP sing 631 n n CAI HAIA NKP sing 632 n n CAL HAL NKP sing 633 n n CAL HALA NKP sing 634 n n CAM HAM NKP sing 635 n n CAM HAMA NKP sing 636 n n CAN HAN NKP sing 637 n n CAN HANA NKP sing 638 n n CAO HAO NKP sing 639 n n CAO HAOA NKP sing 640 e n CAP HAP NKP sing 641 n n CAP HAPA NKP sing 642 n n CAQ HAQ NKP sing 643 n n CAQ HAQA NKP sing 644 n n CAR HAR NKP sing 645 n n CAR HARA NKP sing 646 n n CAS HAS NKP sing 647 n n CAT HAT NKP sing 648 n n CAU HAU NKP sing 649 n n CAU HAUA NKP sing 650 n n CAV HAV NKP sing 651 n n CAV HAVA NKP sing 652 n n CAW HAW NKP sing 653 n n CAW HAWA NKP sing 654 n n CAX HAX NKP sing 655 n n CAX HAXA NKP sing 656 n n CAY HAY NKP sing 657 n n CAY HAYA NKP sing 658 n n CAZ HAZ NKP sing 659 n n CAZ HAZA NKP sing 660 n n CBA HBA NKP sing 661 n n CBA HBAA NKP sing 662 n n CBB HBB NKP sing 663 n n CBB HBBA NKP sing 664 n n CBB HBBB NKP sing 665 n n OBC HOBC NKP sing 666 n n OAA HOAA NKP sing 667 n n OAB HOAB NKP sing 668 n n # _atom_sites.entry_id 8C88 _atom_sites.fract_transf_matrix[1][1] 0.00991 _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] 0.00991 _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] 0.004219 _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 D 4 NKP H 1 301 301 NKP NKP . E 5 LDA H 1 302 702 LDA LDA . F 6 UNL H 1 303 802 UNL UNL . G 6 UNL H 1 304 803 UNL UNL . H 6 UNL H 1 305 804 UNL UNL . I 7 OLC L 1 501 501 OLC OLC . J 8 BCL L 1 502 302 BCL BCL . K 8 BCL L 1 503 304 BCL BCL . L 9 BPH L 1 504 402 BPH BPH . M 6 UNL L 1 505 805 UNL UNL . N 6 UNL L 1 506 807 UNL UNL . O 6 UNL L 1 507 808 UNL UNL . P 10 DIO L 1 508 40 DIO DIO . Q 11 EDO L 1 509 46 EDO EDO . R 11 EDO L 1 510 48 EDO EDO . S 11 EDO L 1 511 50 EDO EDO . T 4 NKP M 1 401 401 NKP NKP . U 8 BCL M 1 402 301 BCL BCL . V 8 BCL M 1 403 303 BCL BCL . W 9 BPH M 1 404 401 BPH BPH . X 12 FE M 1 405 500 FE FE . Y 13 U10 M 1 406 501 U10 U10 . Z 14 SPN M 1 407 600 SPN SPN . AA 5 LDA M 1 408 701 LDA LDA . BA 5 LDA M 1 409 705 LDA LDA . CA 5 LDA M 1 410 709 LDA LDA . DA 5 LDA M 1 411 710 LDA LDA . EA 6 UNL M 1 412 810 UNL UNL . FA 15 PO4 M 1 413 2 PO4 PO4 . GA 15 PO4 M 1 414 3 PO4 PO4 . HA 5 LDA M 1 415 1 LDA LDA . IA 16 HOH H 1 401 21 HOH HOH . IA 16 HOH H 2 402 18 HOH HOH . IA 16 HOH H 3 403 17 HOH HOH . JA 16 HOH L 1 601 9 HOH HOH . JA 16 HOH L 2 602 11 HOH HOH . JA 16 HOH L 3 603 10 HOH HOH . JA 16 HOH L 4 604 4 HOH HOH . JA 16 HOH L 5 605 14 HOH HOH . JA 16 HOH L 6 606 25 HOH HOH . JA 16 HOH L 7 607 5 HOH HOH . JA 16 HOH L 8 608 13 HOH HOH . KA 16 HOH M 1 501 12 HOH HOH . KA 16 HOH M 2 502 8 HOH HOH . KA 16 HOH M 3 503 2 HOH HOH . KA 16 HOH M 4 504 3 HOH HOH . KA 16 HOH M 5 505 6 HOH HOH . KA 16 HOH M 6 506 16 HOH HOH . KA 16 HOH M 7 507 1 HOH HOH . KA 16 HOH M 8 508 24 HOH HOH . KA 16 HOH M 9 509 15 HOH HOH . KA 16 HOH M 10 510 22 HOH HOH . KA 16 HOH M 11 511 7 HOH HOH . KA 16 HOH M 12 512 19 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 OAA NKP . . . D 4 3.607 -47.674 -40.617 1 85.78 ? OAA NKP 301 H 1 HETATM 2 O OAB NKP . . . D 4 6.134 -47.746 -40.224 1 72.26 ? OAB NKP 301 H 1 HETATM 3 P PAC NKP . . . D 4 4.807 -47.028 -39.961 1 83.59 ? PAC NKP 301 H 1 HETATM 4 O OAD NKP . . . D 4 4.876 -45.528 -40.206 1 60.44 ? OAD NKP 301 H 1 HETATM 5 O OAE NKP . . . D 4 6.163 -48.566 -34.87 1 100.14 ? OAE NKP 301 H 1 HETATM 6 O OAF NKP . . . D 4 4.484 -47.291 -38.405 1 103.31 ? OAF NKP 301 H 1 HETATM 7 C CAG NKP . . . D 4 4.239 -48.668 -37.977 1 103.07 ? CAG NKP 301 H 1 HETATM 8 C CAH NKP . . . D 4 5.549 -49.395 -37.769 1 104.26 ? CAH NKP 301 H 1 HETATM 9 C CAI NKP . . . D 4 5.468 -50.446 -36.681 1 107.67 ? CAI NKP 301 H 1 HETATM 10 O OAJ NKP . . . D 4 6.71 -50.464 -35.939 1 103.68 ? OAJ NKP 301 H 1 HETATM 11 C CAK NKP . . . D 4 6.961 -49.434 -35.13 1 100.44 ? CAK NKP 301 H 1 HETATM 12 C CAL NKP . . . D 4 8.367 -49.5 -34.591 1 92.01 ? CAL NKP 301 H 1 HETATM 13 C CAM NKP . . . D 4 8.448 -49.803 -33.124 1 86.99 ? CAM NKP 301 H 1 HETATM 14 C CAN NKP . . . D 4 9.366 -48.842 -32.389 1 73.91 ? CAN NKP 301 H 1 HETATM 15 C CAO NKP . . . D 4 9.815 -49.318 -31.033 1 75.94 ? CAO NKP 301 H 1 HETATM 16 C CAP NKP . . . D 4 10.934 -50.33 -31.078 1 77.01 ? CAP NKP 301 H 1 HETATM 17 C CAQ NKP . . . D 4 11.742 -50.458 -29.787 1 75.72 ? CAQ NKP 301 H 1 HETATM 18 C CAR NKP . . . D 4 11.084 -51.248 -28.696 1 74.71 ? CAR NKP 301 H 1 HETATM 19 C CAS NKP . . . D 4 12.071 -51.884 -27.761 1 80.54 ? CAS NKP 301 H 1 HETATM 20 C CAT NKP . . . D 4 12.31 -53.177 -27.687 1 89.35 ? CAT NKP 301 H 1 HETATM 21 C CAU NKP . . . D 4 13.163 -53.956 -26.726 1 87.98 ? CAU NKP 301 H 1 HETATM 22 C CAV NKP . . . D 4 14.625 -53.584 -26.723 1 92.66 ? CAV NKP 301 H 1 HETATM 23 C CAW NKP . . . D 4 15.545 -54.585 -26.017 1 96.98 ? CAW NKP 301 H 1 HETATM 24 C CAX NKP . . . D 4 16.978 -54.116 -25.796 1 87.58 ? CAX NKP 301 H 1 HETATM 25 C CAY NKP . . . D 4 17.678 -53.583 -27.033 1 83.45 ? CAY NKP 301 H 1 HETATM 26 C CAZ NKP . . . D 4 19.111 -53.166 -26.799 1 82.98 ? CAZ NKP 301 H 1 HETATM 27 C CBA NKP . . . D 4 19.822 -52.531 -27.97 1 78.87 ? CBA NKP 301 H 1 HETATM 28 C CBB NKP . . . D 4 21.282 -52.247 -27.688 1 78.3 ? CBB NKP 301 H 1 HETATM 29 O OBC NKP . . . D 4 5.974 -49.976 -39.006 1 87.51 ? OBC NKP 301 H 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 29 #