data_8C88
#
_model_server_result.job_id            z878tXzhAeBTLD8ozHpYYA 
_model_server_result.datetime_utc      '2024-11-13 06:53:56' 
_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":"T","auth_seq_id":401}' 
#
_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 . . . T 4 -2.265 -47.66 -38.024 1 112.87 ? OAA NKP 401 M 1 
HETATM 2 O OAB NKP . . . T 4 -1.256 -45.683 -39.265 1 75.05 ? OAB NKP 401 M 1 
HETATM 3 P PAC NKP . . . T 4 -1.001 -47.018 -38.592 1 99.02 ? PAC NKP 401 M 1 
HETATM 4 O OAD NKP . . . T 4 -0.217 -47.967 -39.472 1 94.56 ? OAD NKP 401 M 1 
HETATM 5 O OAE NKP . . . T 4 5.675 -43.888 -34.677 1 89.16 ? OAE NKP 401 M 1 
HETATM 6 O OAF NKP . . . T 4 -0.05 -46.719 -37.304 1 106.39 ? OAF NKP 401 M 1 
HETATM 7 C CAG NKP . . . T 4 1.249 -46.088 -37.505 1 93.03 ? CAG NKP 401 M 1 
HETATM 8 C CAH NKP . . . T 4 2.195 -46.395 -36.361 1 95.05 ? CAH NKP 401 M 1 
HETATM 9 C CAI NKP . . . T 4 2.516 -45.209 -35.484 1 90.58 ? CAI NKP 401 M 1 
HETATM 10 O OAJ NKP . . . T 4 3.948 -45.012 -35.536 1 101.02 ? OAJ NKP 401 M 1 
HETATM 11 C CAK NKP . . . T 4 4.494 -44.152 -34.671 1 99.43 ? CAK NKP 401 M 1 
HETATM 12 C CAL NKP . . . T 4 3.468 -43.573 -33.705 1 93.07 ? CAL NKP 401 M 1 
HETATM 13 C CAM NKP . . . T 4 4.044 -42.746 -32.582 1 76.85 ? CAM NKP 401 M 1 
HETATM 14 C CAN NKP . . . T 4 4.25 -43.55 -31.312 1 73.64 ? CAN NKP 401 M 1 
HETATM 15 C CAO NKP . . . T 4 2.968 -44.078 -30.731 1 80.43 ? CAO NKP 401 M 1 
HETATM 16 C CAP NKP . . . T 4 2.096 -43.003 -30.137 1 84.43 ? CAP NKP 401 M 1 
HETATM 17 C CAQ NKP . . . T 4 2.512 -42.53 -28.745 1 71.96 ? CAQ NKP 401 M 1 
HETATM 18 C CAR NKP . . . T 4 2.243 -43.51 -27.644 1 65.55 ? CAR NKP 401 M 1 
HETATM 19 C CAS NKP . . . T 4 1.193 -43.062 -26.671 1 70.86 ? CAS NKP 401 M 1 
HETATM 20 C CAT NKP . . . T 4 0.768 -43.775 -25.649 1 66.77 ? CAT NKP 401 M 1 
HETATM 21 C CAU NKP . . . T 4 -0.188 -43.303 -24.596 1 71.15 ? CAU NKP 401 M 1 
HETATM 22 C CAV NKP . . . T 4 0.228 -43.618 -23.183 1 73.85 ? CAV NKP 401 M 1 
HETATM 23 C CAW NKP . . . T 4 0.073 -45.08 -22.788 1 73.47 ? CAW NKP 401 M 1 
HETATM 24 C CAX NKP . . . T 4 0.504 -45.43 -21.37 1 77.11 ? CAX NKP 401 M 1 
HETATM 25 C CAY NKP . . . T 4 1.979 -45.226 -21.066 1 77.73 ? CAY NKP 401 M 1 
HETATM 26 C CAZ NKP . . . T 4 2.592 -46.3 -20.181 1 76.27 ? CAZ NKP 401 M 1 
HETATM 27 C CBA NKP . . . T 4 1.836 -46.618 -18.919 1 71.52 ? CBA NKP 401 M 1 
HETATM 28 C CBB NKP . . . T 4 2.436 -47.726 -18.077 1 76.85 ? CBB NKP 401 M 1 
HETATM 29 O OBC NKP . . . T 4 1.71 -47.47 -35.556 1 103.95 ? OBC NKP 401 M 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           242 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           29 
#