data_8C88
#
_model_server_result.job_id            18lOh4K_A2BnULYVKLBj2Q 
_model_server_result.datetime_utc      '2024-11-13 07:00:24' 
_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           14 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           273 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           29 
#