data_9B4E
#
_model_server_result.job_id            VgbTMtIL8-Negknu2SyjKg 
_model_server_result.datetime_utc      '2024-10-18 22:24:27' 
_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          9b4e 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":602}' 
#
_entry.id    9B4E 
#
_exptl.entry_id    9B4E 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              792.075 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine 
_entity.pdbx_number_of_molecules    4 
_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            9B4E 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9B4E 
_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        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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
? 2 C N N 
? 2 D N N 
? 2 K N N 
? 2 L 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 A SG CYS 153 A CYS 153 1_555 A SG CYS 213 A CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf2 B SG CYS 153 B CYS 153 1_555 B SG CYS 213 B CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc1 A OE2 GLU 197 A GLU 197 1_555 H CA CA . A CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? 
metalc ? metalc2 A OE1 GLU 200 A GLU 200 1_555 H CA CA . A CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? 
metalc ? metalc3 A OE1 GLN 217 A GLN 217 1_555 H CA CA . A CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? 
metalc ? metalc4 A OD2 ASP 221 A ASP 221 1_555 H CA CA . A CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? 
metalc ? metalc5 B OE2 GLU 197 B GLU 197 1_555 P CA CA . B CA 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.748 ? 
metalc ? metalc6 B OE1 GLU 200 B GLU 200 1_555 P CA CA . B CA 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? 
metalc ? metalc7 B OE1 GLN 217 B GLN 217 1_555 P CA CA . B CA 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? 
metalc ? metalc8 B OD2 ASP 221 B ASP 221 1_555 P CA CA . B CA 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? 
#
_chem_comp.formula           'C42 H82 N O10 P' 
_chem_comp.formula_weight    792.075 
_chem_comp.id                P5S 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'phosphatidyl serine' 
#
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
CA C P5S sing 628 n n 
O C P5S doub 629 n n 
C OXT P5S sing 630 n n 
CA N P5S sing 631 n n 
N HN P5S sing 632 n n 
N HNA P5S sing 633 n n 
O19 C1 P5S sing 634 n n 
C1 C2 P5S sing 635 n n 
C1 H1 P5S sing 636 n n 
C1 H1A P5S sing 637 n n 
C2 O37 P5S sing 638 n n 
C2 C3 P5S sing 639 n n 
C2 H2 P5S sing 640 n n 
O16 C3 P5S sing 641 n n 
C3 H3 P5S sing 642 n n 
C3 H3A P5S sing 643 n n 
CB CA P5S sing 644 n n 
CA HA P5S sing 645 n n 
CB OG P5S sing 646 n n 
CB HB P5S sing 647 n n 
CB HBA P5S sing 648 n n 
P12 OG P5S sing 649 n n 
O16 P12 P5S sing 650 n n 
O13 P12 P5S doub 651 n n 
P12 O15 P5S sing 652 n n 
O15 HO15 P5S sing 653 n n 
C20 C17 P5S sing 654 n n 
O19 C17 P5S sing 655 n n 
C17 O18 P5S doub 656 n n 
C21 C20 P5S sing 657 n n 
C20 H20 P5S sing 658 n n 
C20 H20A P5S sing 659 n n 
C21 C22 P5S sing 660 n n 
C21 H21 P5S sing 661 n n 
C21 H21A P5S sing 662 n n 
C23 C22 P5S sing 663 n n 
C22 H22 P5S sing 664 n n 
C22 H22A P5S sing 665 n n 
C24 C23 P5S sing 666 n n 
C23 H23 P5S sing 667 n n 
C23 H23A P5S sing 668 n n 
C25 C24 P5S sing 669 n n 
C24 H24 P5S sing 670 n n 
C24 H24A P5S sing 671 n n 
C26 C25 P5S sing 672 n n 
C25 H25 P5S sing 673 n n 
C25 H25A P5S sing 674 n n 
C26 C27 P5S sing 675 n n 
C26 H26 P5S sing 676 n n 
C26 H26A P5S sing 677 n n 
C27 C28 P5S sing 678 n n 
C27 H27 P5S sing 679 n n 
C27 H27A P5S sing 680 n n 
C29 C28 P5S sing 681 n n 
C28 H28 P5S sing 682 n n 
C28 H28A P5S sing 683 n n 
C30 C29 P5S sing 684 n n 
C29 H29 P5S sing 685 n n 
C29 H29A P5S sing 686 n n 
C31 C30 P5S sing 687 n n 
C30 H30 P5S sing 688 n n 
C30 H30A P5S sing 689 n n 
C31 C32 P5S sing 690 n n 
C31 H31 P5S sing 691 n n 
C31 H31A P5S sing 692 n n 
C33 C32 P5S sing 693 n n 
C32 H32 P5S sing 694 n n 
C32 H32A P5S sing 695 n n 
C33 C34 P5S sing 696 n n 
C33 H33 P5S sing 697 n n 
C33 H33A P5S sing 698 n n 
C35 C34 P5S sing 699 n n 
C34 H34 P5S sing 700 n n 
C34 H34A P5S sing 701 n n 
C36 C35 P5S sing 702 n n 
C35 H35 P5S sing 703 n n 
C35 H35A P5S sing 704 n n 
C36 H36 P5S sing 705 n n 
C36 H36A P5S sing 706 n n 
C36 H36B P5S sing 707 n n 
C38 O37 P5S sing 708 n n 
O47 C38 P5S doub 709 n n 
C38 C39 P5S sing 710 n n 
C40 C39 P5S sing 711 n n 
C39 H39 P5S sing 712 n n 
C39 H39A P5S sing 713 n n 
C41 C40 P5S sing 714 n n 
C40 H40 P5S sing 715 n n 
C40 H40A P5S sing 716 n n 
C42 C41 P5S sing 717 n n 
C41 H41 P5S sing 718 n n 
C41 H41A P5S sing 719 n n 
C43 C42 P5S sing 720 n n 
C42 H42 P5S sing 721 n n 
C42 H42A P5S sing 722 n n 
C43 C44 P5S sing 723 n n 
C43 H43 P5S sing 724 n n 
C43 H43A P5S sing 725 n n 
C44 C45 P5S sing 726 n n 
C44 H44 P5S sing 727 n n 
C44 H44A P5S sing 728 n n 
C45 C46 P5S sing 729 n n 
C45 H45 P5S sing 730 n n 
C45 H45A P5S sing 731 n n 
C46 C48 P5S sing 732 n n 
C46 H46 P5S sing 733 n n 
C46 H46A P5S sing 734 n n 
C48 C49 P5S sing 735 n n 
C48 H48 P5S sing 736 n n 
C48 H48A P5S sing 737 n n 
C49 C50 P5S sing 738 n n 
C49 H49 P5S sing 739 n n 
C49 H49A P5S sing 740 n n 
C50 C51 P5S sing 741 n n 
C50 H50 P5S sing 742 n n 
C50 H50A P5S sing 743 n n 
C51 C52 P5S sing 744 n n 
C51 H51 P5S sing 745 n n 
C51 H51A P5S sing 746 n n 
C53 C52 P5S sing 747 n n 
C52 H52 P5S sing 748 n n 
C52 H52A P5S sing 749 n n 
C53 C54 P5S sing 750 n n 
C53 H53 P5S sing 751 n n 
C53 H53A P5S sing 752 n n 
C55 C54 P5S sing 753 n n 
C54 H54 P5S sing 754 n n 
C54 H54A P5S sing 755 n n 
C55 C56 P5S sing 756 n n 
C55 H55 P5S sing 757 n n 
C55 H55A P5S sing 758 n n 
C56 H56 P5S sing 759 n n 
C56 H56A P5S sing 760 n n 
C56 H56B P5S sing 761 n n 
OXT HXT P5S sing 762 n n 
#
_atom_sites.entry_id                     9B4E 
_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
C 2 P5S A 1 501 500 P5S P5S . 
D 2 P5S A 1 502 501 P5S P5S . 
E 3 LBN A 1 503 602 LBN LBN . 
F 4 A1AIS A 1 504 701 A1AIS DPI . 
G 5 6OU A 1 505 801 6OU PPE . 
H 6 CA A 1 506 901 CA CA . 
I 3 LBN A 1 507 601 LBN LBN . 
J 3 LBN B 1 601 601 LBN LBN . 
K 2 P5S B 1 602 500 P5S P5S . 
L 2 P5S B 1 603 501 P5S P5S . 
M 3 LBN B 1 604 602 LBN LBN . 
N 4 A1AIS B 1 605 701 A1AIS DPI . 
O 5 6OU B 1 606 801 6OU PPE . 
P 6 CA B 1 607 901 CA CA . 
Q 7 HOH A 1 601 1146 HOH HOH . 
Q 7 HOH A 2 602 1111 HOH HOH . 
Q 7 HOH A 3 603 1126 HOH HOH . 
Q 7 HOH A 4 604 1143 HOH HOH . 
Q 7 HOH A 5 605 1114 HOH HOH . 
Q 7 HOH A 6 606 1141 HOH HOH . 
Q 7 HOH A 7 607 1103 HOH HOH . 
Q 7 HOH A 8 608 1134 HOH HOH . 
R 7 HOH B 1 701 1146 HOH HOH . 
R 7 HOH B 2 702 1126 HOH HOH . 
R 7 HOH B 3 703 1111 HOH HOH . 
R 7 HOH B 4 704 1143 HOH HOH . 
R 7 HOH B 5 705 1114 HOH HOH . 
R 7 HOH B 6 706 1141 HOH HOH . 
R 7 HOH B 7 707 1103 HOH HOH . 
R 7 HOH B 8 708 1134 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 C C P5S . . . K 2 116.014 143.145 132.405 1 46.55 ? C P5S 602 B 1 
HETATM 2 N N P5S . . . K 2 116.898 141.771 134.182 1 46.55 ? N P5S 602 B 1 
HETATM 3 O O P5S . . . K 2 115.314 143.349 131.38 1 46.55 ? O P5S 602 B 1 
HETATM 4 C C1 P5S . . . K 2 113.092 141.966 127.121 1 46.55 ? C1 P5S 602 B 1 
HETATM 5 C C2 P5S . . . K 2 112.255 141.14 128.107 1 46.55 ? C2 P5S 602 B 1 
HETATM 6 C C3 P5S . . . K 2 113.209 140.452 129.054 1 46.55 ? C3 P5S 602 B 1 
HETATM 7 C CA P5S . . . K 2 116.277 141.725 132.877 1 46.55 ? CA P5S 602 B 1 
HETATM 8 C CB P5S . . . K 2 114.953 140.982 132.97 1 46.55 ? CB P5S 602 B 1 
HETATM 9 O OG P5S . . . K 2 114.57 140.611 131.686 1 46.55 ? OG P5S 602 B 1 
HETATM 10 P P12 P5S . . . K 2 113.3 139.598 131.536 1 46.55 ? P12 P5S 602 B 1 
HETATM 11 O O13 P5S . . . K 2 113.796 138.181 131.506 1 46.55 ? O13 P5S 602 B 1 
HETATM 12 O O15 P5S . . . K 2 112.386 139.78 132.714 1 46.55 ? O15 P5S 602 B 1 
HETATM 13 O O16 P5S . . . K 2 112.481 139.929 130.138 1 46.55 ? O16 P5S 602 B 1 
HETATM 14 C C17 P5S . . . K 2 113.533 144.211 126.498 1 46.55 ? C17 P5S 602 B 1 
HETATM 15 O O18 P5S . . . K 2 114.688 144.213 126.756 1 46.55 ? O18 P5S 602 B 1 
HETATM 16 O O19 P5S . . . K 2 112.663 143.314 127.184 1 46.55 ? O19 P5S 602 B 1 
HETATM 17 C C20 P5S . . . K 2 112.978 145.176 125.418 1 46.55 ? C20 P5S 602 B 1 
HETATM 18 C C21 P5S . . . K 2 111.996 144.477 124.472 1 46.55 ? C21 P5S 602 B 1 
HETATM 19 C C22 P5S . . . K 2 112.545 144.326 123.045 1 46.55 ? C22 P5S 602 B 1 
HETATM 20 C C23 P5S . . . K 2 112.076 143.027 122.393 1 46.55 ? C23 P5S 602 B 1 
HETATM 21 C C24 P5S . . . K 2 112.88 142.662 121.147 1 46.55 ? C24 P5S 602 B 1 
HETATM 22 C C25 P5S . . . K 2 113.18 141.155 121.085 1 46.55 ? C25 P5S 602 B 1 
HETATM 23 C C26 P5S . . . K 2 112.546 140.464 119.86 1 46.55 ? C26 P5S 602 B 1 
HETATM 24 C C27 P5S . . . K 2 113.303 139.176 119.454 1 46.55 ? C27 P5S 602 B 1 
HETATM 25 C C28 P5S . . . K 2 112.844 138.638 118.072 1 46.55 ? C28 P5S 602 B 1 
HETATM 26 C C29 P5S . . . K 2 113.971 138.7 117.009 1 46.55 ? C29 P5S 602 B 1 
HETATM 27 C C30 P5S . . . K 2 113.724 137.749 115.831 1 46.55 ? C30 P5S 602 B 1 
HETATM 28 C C31 P5S . . . K 2 113.821 138.463 114.475 1 46.55 ? C31 P5S 602 B 1 
HETATM 29 C C32 P5S . . . K 2 113.868 137.487 113.3 1 46.55 ? C32 P5S 602 B 1 
HETATM 30 C C33 P5S . . . K 2 113.219 138.063 112.05 1 46.55 ? C33 P5S 602 B 1 
HETATM 31 O O37 P5S . . . K 2 111.53 140.168 127.393 1 46.55 ? O37 P5S 602 B 1 
HETATM 32 C C38 P5S . . . K 2 110.329 140.641 126.791 1 46.55 ? C38 P5S 602 B 1 
HETATM 33 C C39 P5S . . . K 2 110.22 140.729 125.241 1 46.55 ? C39 P5S 602 B 1 
HETATM 34 C C40 P5S . . . K 2 108.934 140.085 124.682 1 46.55 ? C40 P5S 602 B 1 
HETATM 35 C C41 P5S . . . K 2 108.822 140.308 123.153 1 46.55 ? C41 P5S 602 B 1 
HETATM 36 C C42 P5S . . . K 2 107.742 139.418 122.492 1 46.55 ? C42 P5S 602 B 1 
HETATM 37 C C43 P5S . . . K 2 108.352 138.177 121.787 1 46.55 ? C43 P5S 602 B 1 
HETATM 38 C C44 P5S . . . K 2 107.253 137.203 121.261 1 46.55 ? C44 P5S 602 B 1 
HETATM 39 C C45 P5S . . . K 2 107.837 136.109 120.308 1 46.55 ? C45 P5S 602 B 1 
HETATM 40 C C46 P5S . . . K 2 106.932 134.833 120.261 1 46.55 ? C46 P5S 602 B 1 
HETATM 41 O O47 P5S . . . K 2 109.42 140.978 127.457 1 46.55 ? O47 P5S 602 B 1 
HETATM 42 C C48 P5S . . . K 2 107.055 134.074 118.914 1 46.55 ? C48 P5S 602 B 1 
HETATM 43 O OXT P5S . . . K 2 116.501 144.112 133.043 1 46.55 ? OXT P5S 602 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           331 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           43 
#