data_7TYT
#
_model_server_result.job_id            3jrEE9q71DnMBxHISotPAQ 
_model_server_result.datetime_utc      '2024-11-05 19:37:26' 
_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          7tyt 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"W","auth_seq_id":1607}' 
#
_entry.id    7TYT 
#
_exptl.entry_id    7TYT 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              792.075 
_entity.id                          7 
_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    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            7TYT 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7TYT 
_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    pentameric 
_pdbx_struct_assembly.oligomeric_count      5 
_pdbx_struct_assembly.details               author_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 
_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    ? 
_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
? 7 L N N 
? 7 W N N 
#
_pdbx_entity_branch.entity_id    3 
_pdbx_entity_branch.type         oligosaccharide 
#
_pdbx_entity_branch_link.link_id                     1 
_pdbx_entity_branch_link.details                     ? 
_pdbx_entity_branch_link.entity_id                   3 
_pdbx_entity_branch_link.entity_branch_list_num_1    2 
_pdbx_entity_branch_link.entity_branch_list_num_2    1 
_pdbx_entity_branch_link.comp_id_1                   NAG 
_pdbx_entity_branch_link.comp_id_2                   NAG 
_pdbx_entity_branch_link.atom_id_1                   C1 
_pdbx_entity_branch_link.leaving_atom_id_1           O1 
_pdbx_entity_branch_link.atom_stereo_config_1        . 
_pdbx_entity_branch_link.atom_id_2                   O4 
_pdbx_entity_branch_link.leaving_atom_id_2           HO4 
_pdbx_entity_branch_link.atom_stereo_config_2        . 
_pdbx_entity_branch_link.value_order                 sing 
#
loop_
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.hetero
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.auth_mon_id
3 n F NAG 1 F 1 NAG E 2010 NAG 
3 n F NAG 2 F 2 NAG E 2011 NAG 
#
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 110 A CYS 110 1_555 A SG CYS 142 A CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf2 B SG CYS 110 B CYS 110 1_555 B SG CYS 142 B CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf3 C SG CYS 110 C CYS 110 1_555 C SG CYS 142 C CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf4 D SG CYS 110 D CYS 110 1_555 D SG CYS 142 D CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf5 E SG CYS 6 E CYS 6 1_555 E SG CYS 26 E CYS 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
covale ? covale1 E ND2 ASN 10 E ASN 10 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? 
covale ? covale2 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? 
metalc ? metalc1 A O THR 130 A THR 130 1_555 H K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? 
metalc ? metalc2 A OG1 THR 130 A THR 130 1_555 H K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.257 ? 
metalc ? metalc3 H K K . A K 402 1_555 B O THR 130 B THR 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? 
metalc ? metalc4 H K K . A K 402 1_555 B OG1 THR 130 B THR 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.489 ? 
metalc ? metalc5 H K K . A K 402 1_555 C O THR 130 C THR 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.586 ? 
metalc ? metalc6 H K K . A K 402 1_555 C OG1 THR 130 C THR 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.395 ? 
metalc ? metalc7 H K K . A K 402 1_555 D O THR 130 D THR 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? 
#
_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' 
#
_atom_sites.entry_id                     7TYT 
_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
G 4 ATP A 1 401 401 ATP ATP . 
H 5 K A 1 402 504 K K . 
I 6 POV A 1 403 505 POV POV . 
J 4 ATP B 1 401 401 ATP ATP . 
K 6 POV B 1 402 505 POV POV . 
L 7 P5S B 1 403 506 P5S P5S . 
M 4 ATP B 1 404 401 ATP ATP . 
N 6 POV C 1 401 505 POV POV . 
O 4 ATP D 1 401 401 ATP ATP . 
P 6 POV D 1 402 505 POV POV . 
Q 8 PTY E 1 1601 506 PTY PTY . 
R 9 BJX E 1 1602 2001 BJX BJX . 
S 4 ATP E 1 1603 2002 ATP ATP . 
T 8 PTY E 1 1604 2003 PTY PTY . 
U 8 PTY E 1 1605 2004 PTY PTY . 
V 8 PTY E 1 1606 2005 PTY PTY . 
W 7 P5S E 1 1607 2006 P5S P5S . 
X 6 POV E 1 1608 2007 POV POV . 
Y 8 PTY E 1 1609 2008 PTY PTY . 
Z 8 PTY E 1 1610 2009 PTY PTY . 
#
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 . . . W 7 200.443 187.097 152.572 1 37.05 ? C P5S 1607 E 1 
HETATM 2 N N P5S . . . W 7 202.451 186.659 154.051 1 37.05 ? N P5S 1607 E 1 
HETATM 3 O O P5S . . . W 7 200.896 187.972 151.808 1 37.05 ? O P5S 1607 E 1 
HETATM 4 C C1 P5S . . . W 7 201.416 186.025 160.962 1 37.05 ? C1 P5S 1607 E 1 
HETATM 5 C C2 P5S . . . W 7 201.796 185.336 159.672 1 37.05 ? C2 P5S 1607 E 1 
HETATM 6 C C3 P5S . . . W 7 200.713 184.495 159.024 1 37.05 ? C3 P5S 1607 E 1 
HETATM 7 C CA P5S . . . W 7 201.45 186.084 153.175 1 37.05 ? CA P5S 1607 E 1 
HETATM 8 C CB P5S . . . W 7 200.66 185.017 153.922 1 37.05 ? CB P5S 1607 E 1 
HETATM 9 O OG P5S . . . W 7 200.521 185.341 155.291 1 37.05 ? OG P5S 1607 E 1 
HETATM 10 P P12 P5S . . . W 7 201.37 184.577 156.458 1 37.05 ? P12 P5S 1607 E 1 
HETATM 11 O O13 P5S . . . W 7 201.278 183.091 156.345 1 37.05 ? O13 P5S 1607 E 1 
HETATM 12 O O15 P5S . . . W 7 202.705 185.248 156.595 1 37.05 ? O15 P5S 1607 E 1 
HETATM 13 O O16 P5S . . . W 7 200.406 184.945 157.731 1 37.05 ? O16 P5S 1607 E 1 
HETATM 14 C C17 P5S . . . W 7 202.396 186.447 163.051 1 37.05 ? C17 P5S 1607 E 1 
HETATM 15 O O18 P5S . . . W 7 202.629 187.542 163.498 1 37.05 ? O18 P5S 1607 E 1 
HETATM 16 O O19 P5S . . . W 7 202.571 186.147 161.776 1 37.05 ? O19 P5S 1607 E 1 
HETATM 17 C C20 P5S . . . W 7 201.892 185.282 163.847 1 37.05 ? C20 P5S 1607 E 1 
HETATM 18 C C21 P5S . . . W 7 201.943 185.559 165.337 1 37.05 ? C21 P5S 1607 E 1 
HETATM 19 C C22 P5S . . . W 7 201.838 184.296 166.179 1 37.05 ? C22 P5S 1607 E 1 
HETATM 20 C C23 P5S . . . W 7 202.045 184.605 167.654 1 37.05 ? C23 P5S 1607 E 1 
HETATM 21 C C24 P5S . . . W 7 202.083 183.382 168.561 1 37.05 ? C24 P5S 1607 E 1 
HETATM 22 C C25 P5S . . . W 7 201.83 183.762 170.012 1 37.05 ? C25 P5S 1607 E 1 
HETATM 23 C C26 P5S . . . W 7 201.935 182.607 170.995 1 37.05 ? C26 P5S 1607 E 1 
HETATM 24 C C27 P5S . . . W 7 200.944 182.78 172.133 1 37.05 ? C27 P5S 1607 E 1 
HETATM 25 C C28 P5S . . . W 7 201.397 182.252 173.484 1 37.05 ? C28 P5S 1607 E 1 
HETATM 26 C C29 P5S . . . W 7 202.496 183.117 174.082 1 37.05 ? C29 P5S 1607 E 1 
HETATM 27 C C30 P5S . . . W 7 202.441 183.209 175.598 1 37.05 ? C30 P5S 1607 E 1 
HETATM 28 C C31 P5S . . . W 7 203.647 183.928 176.183 1 37.05 ? C31 P5S 1607 E 1 
HETATM 29 C C32 P5S . . . W 7 203.259 185.078 177.1 1 37.05 ? C32 P5S 1607 E 1 
HETATM 30 C C33 P5S . . . W 7 202.07 184.752 177.993 1 37.05 ? C33 P5S 1607 E 1 
HETATM 31 C C34 P5S . . . W 7 201.804 185.822 179.041 1 37.05 ? C34 P5S 1607 E 1 
HETATM 32 C C35 P5S . . . W 7 200.667 185.46 179.986 1 37.05 ? C35 P5S 1607 E 1 
HETATM 33 C C36 P5S . . . W 7 200.74 186.21 181.307 1 37.05 ? C36 P5S 1607 E 1 
HETATM 34 O O37 P5S . . . W 7 202.991 184.578 159.914 1 37.05 ? O37 P5S 1607 E 1 
HETATM 35 C C38 P5S . . . W 7 202.934 183.4 160.532 1 37.05 ? C38 P5S 1607 E 1 
HETATM 36 C C39 P5S . . . W 7 203.949 182.438 159.989 1 37.05 ? C39 P5S 1607 E 1 
HETATM 37 C C40 P5S . . . W 7 203.691 181.042 160.525 1 37.05 ? C40 P5S 1607 E 1 
HETATM 38 C C41 P5S . . . W 7 204.48 180.784 161.795 1 37.05 ? C41 P5S 1607 E 1 
HETATM 39 C C42 P5S . . . W 7 203.549 180.494 162.963 1 37.05 ? C42 P5S 1607 E 1 
HETATM 40 C C43 P5S . . . W 7 204.138 180.896 164.303 1 37.05 ? C43 P5S 1607 E 1 
HETATM 41 C C44 P5S . . . W 7 203.12 180.847 165.431 1 37.05 ? C44 P5S 1607 E 1 
HETATM 42 C C45 P5S . . . W 7 202.826 179.442 165.925 1 37.05 ? C45 P5S 1607 E 1 
HETATM 43 C C46 P5S . . . W 7 202.762 179.378 167.445 1 37.05 ? C46 P5S 1607 E 1 
HETATM 44 O O47 P5S . . . W 7 202.175 183.127 161.428 1 37.05 ? O47 P5S 1607 E 1 
HETATM 45 C C48 P5S . . . W 7 202.621 177.959 167.974 1 37.05 ? C48 P5S 1607 E 1 
HETATM 46 C C49 P5S . . . W 7 202.529 177.886 169.492 1 37.05 ? C49 P5S 1607 E 1 
HETATM 47 C C50 P5S . . . W 7 202.289 176.471 169.996 1 37.05 ? C50 P5S 1607 E 1 
HETATM 48 C C51 P5S . . . W 7 201.548 176.431 171.324 1 37.05 ? C51 P5S 1607 E 1 
HETATM 49 C C52 P5S . . . W 7 202.406 176.805 172.525 1 37.05 ? C52 P5S 1607 E 1 
HETATM 50 C C53 P5S . . . W 7 201.628 177.567 173.588 1 37.05 ? C53 P5S 1607 E 1 
HETATM 51 C C54 P5S . . . W 7 201.619 176.874 174.944 1 37.05 ? C54 P5S 1607 E 1 
HETATM 52 C C55 P5S . . . W 7 200.533 177.409 175.87 1 37.05 ? C55 P5S 1607 E 1 
HETATM 53 C C56 P5S . . . W 7 199.901 176.326 176.731 1 37.05 ? C56 P5S 1607 E 1 
HETATM 54 O OXT P5S . . . W 7 199.248 186.951 152.905 1 37.05 ? OXT P5S 1607 E 1 
#
_model_server_stats.io_time_ms              33 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    62 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           54 
#