data_5XTD
#
_model_server_result.job_id            k6GOzmuWE5he-dH2z1tbMg 
_model_server_result.datetime_utc      '2024-11-26 18:51:36' 
_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          5xtd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"IB","auth_seq_id":203}' 
#
_entry.id    5XTD 
#
_exptl.entry_id    5XTD 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              767.132 
_entity.id                          47 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL 
_entity.pdbx_number_of_molecules    9 
_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            5XTD 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5XTD 
_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    45-meric 
_pdbx_struct_assembly.oligomeric_count      45 
_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,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB,NB,OB,PB,QB,RB,SB,TB,UB,VB,WB 
_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
? 47 XA N N 
? 47 FB N N 
? 47 IB N N 
? 47 KB N N 
? 47 LB N N 
? 47 MB N N 
? 47 NB N N 
? 47 VB N N 
? 47 WB 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 T SG CYS 94 V CYS 95 1_555 T SG CYS 114 V CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf2 AA SG CYS 111 c CYS 144 1_555 JA SG CYS 279 l CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
disulf ? disulf3 BA SG CYS 149 d CYS 149 1_555 CA SG CYS 88 e CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf4 FA SG CYS 32 h CYS 33 1_555 FA SG CYS 65 h CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf5 FA SG CYS 42 h CYS 43 1_555 FA SG CYS 55 h CYS 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf6 QA SG CYS 75 u CYS 78 1_555 QA SG CYS 107 u CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? 
disulf ? disulf7 RA SG CYS 69 v CYS 69 1_555 RA SG CYS 80 v CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? 
metalc ? metalc1 A NE2 GLN 355 A GLN 381 1_555 TA FE1 SF4 . A SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? 
metalc ? metalc2 B N CYS 80 B CYS 114 1_555 VA FE2 SF4 . B SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? 
metalc ? metalc3 B N GLY 120 B GLY 154 1_555 WA FE4 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.794 ? 
metalc ? metalc4 C SG CYS 32 C CYS 89 1_555 YA FE2 SF4 . C SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? 
metalc ? metalc5 L NE2 HIS 95 M HIS 124 1_555 BB FE3 SF4 . M SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? 
metalc ? metalc6 L SG CYS 108 M CYS 137 1_555 BB FE4 SF4 . M SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? 
covale ? covale1 L SG CYS 147 M CYS 176 1_555 CB S3 SF4 . M SF4 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? 
metalc ? metalc7 L SG CYS 147 M CYS 176 1_555 CB FE1 SF4 . M SF4 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? 
metalc ? metalc8 L O CYS 150 M CYS 179 1_555 CB FE1 SF4 . M SF4 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.567 ? 
metalc ? metalc9 N SG CYS 141 O CYS 176 1_555 EB FE2 FES . O FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? 
metalc ? metalc10 N SG CYS 145 O CYS 180 1_555 EB FE2 FES . O FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? 
#
_chem_comp.formula           'C42 H89 N O8 P 1' 
_chem_comp.formula_weight    767.132 
_chem_comp.id                PLX 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     5XTD 
_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
TA 45 SF4 A 1 501 501 SF4 SF4 . 
UA 46 FMN A 1 502 502 FMN FMN . 
VA 45 SF4 B 1 301 301 SF4 SF4 . 
WA 45 SF4 B 1 302 302 SF4 SF4 . 
XA 47 PLX B 1 303 401 PLX PLX . 
YA 45 SF4 C 1 301 301 SF4 SF4 . 
ZA 48 8Q1 E 1 201 201 8Q1 8Q1 . 
AB 49 NDP J 1 401 401 NDP NDP . 
BB 45 SF4 M 1 801 801 SF4 SF4 . 
CB 45 SF4 M 1 802 802 SF4 SF4 . 
DB 50 FES M 1 803 803 FES FES . 
EB 50 FES O 1 301 301 FES FES . 
FB 47 PLX U 1 101 101 PLX PLX . 
GB 51 CDL V 1 201 201 CDL CDL . 
HB 52 PEE V 1 202 202 PEE PEE . 
IB 47 PLX V 1 203 203 PLX PLX . 
JB 52 PEE W 1 201 201 PEE PEE . 
KB 47 PLX b 1 201 201 PLX PLX . 
LB 47 PLX g 1 201 201 PLX PLX . 
MB 47 PLX g 1 202 202 PLX PLX . 
NB 47 PLX g 1 203 203 PLX PLX . 
OB 51 CDL i 1 401 401 CDL CDL . 
PB 52 PEE l 1 701 701 PEE PEE . 
QB 52 PEE l 1 702 702 PEE PEE . 
RB 51 CDL l 1 703 703 CDL CDL . 
SB 51 CDL l 1 704 704 CDL CDL . 
TB 51 CDL n 1 101 101 CDL CDL . 
UB 48 8Q1 p 1 201 201 8Q1 8Q1 . 
VB 47 PLX r 1 501 501 PLX PLX . 
WB 47 PLX r 1 502 502 PLX PLX . 
#
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 C23 PLX . . . IB 47 278.067 246.95 242.167 1 40.69 ? C23 PLX 203 V 1 
HETATM 2 C C22 PLX . . . IB 47 277.013 247.9 242.763 1 41.04 ? C22 PLX 203 V 1 
HETATM 3 C C21 PLX . . . IB 47 276.067 247.209 243.774 1 40.14 ? C21 PLX 203 V 1 
HETATM 4 C C20 PLX . . . IB 47 274.955 248.155 244.302 1 40.19 ? C20 PLX 203 V 1 
HETATM 5 C C19 PLX . . . IB 47 274.529 247.835 245.756 1 37.39 ? C19 PLX 203 V 1 
HETATM 6 C C18 PLX . . . IB 47 273.162 248.449 246.149 1 33.56 ? C18 PLX 203 V 1 
HETATM 7 C C17 PLX . . . IB 47 272.043 248.072 245.159 1 31.18 ? C17 PLX 203 V 1 
HETATM 8 C C16 PLX . . . IB 47 270.695 247.785 245.853 1 31.66 ? C16 PLX 203 V 1 
HETATM 9 C C15 PLX . . . IB 47 270.241 248.94 246.765 1 33.01 ? C15 PLX 203 V 1 
HETATM 10 C C14 PLX . . . IB 47 268.707 249.064 246.841 1 32.58 ? C14 PLX 203 V 1 
HETATM 11 C C13 PLX . . . IB 47 267.999 247.698 246.764 1 31.76 ? C13 PLX 203 V 1 
HETATM 12 C C12 PLX . . . IB 47 266.774 247.604 247.696 1 32.14 ? C12 PLX 203 V 1 
HETATM 13 C C11 PLX . . . IB 47 267.082 246.878 249.024 1 32.89 ? C11 PLX 203 V 1 
HETATM 14 C C10 PLX . . . IB 47 266.192 245.632 249.204 1 33.8 ? C10 PLX 203 V 1 
HETATM 15 C C9 PLX . . . IB 47 266.324 245.001 250.611 1 35.24 ? C9 PLX 203 V 1 
HETATM 16 C C8 PLX . . . IB 47 265.822 245.942 251.73 1 36.45 ? C8 PLX 203 V 1 
HETATM 17 C C7 PLX . . . IB 47 265.026 245.214 252.839 1 37.52 ? C7 PLX 203 V 1 
HETATM 18 C C6 PLX . . . IB 47 263.737 245.96 253.191 1 36.56 ? C6 PLX 203 V 1 
HETATM 19 O O7 PLX . . . IB 47 262.701 245.052 253.423 1 37.4 ? O7 PLX 203 V 1 
HETATM 20 O O6 PLX . . . IB 47 263.927 246.781 254.329 1 33.47 ? O6 PLX 203 V 1 
HETATM 21 C C4 PLX . . . IB 47 263.275 248.019 254.215 1 30.66 ? C4 PLX 203 V 1 
HETATM 22 C C3 PLX . . . IB 47 262.898 248.54 255.59 1 27.81 ? C3 PLX 203 V 1 
HETATM 23 O O4 PLX . . . IB 47 262.36 249.86 255.432 1 22.36 ? O4 PLX 203 V 1 
HETATM 24 P P1 PLX . . . IB 47 261.318 250.419 256.517 1 19.23 ? P1 PLX 203 V 1 
HETATM 25 O O1 PLX . . . IB 47 261.016 251.973 256.246 1 14.54 ? O1 PLX 203 V 1 
HETATM 26 C C2 PLX . . . IB 47 260.084 252.381 255.231 1 9.09 ? C2 PLX 203 V 1 
HETATM 27 C C1 PLX . . . IB 47 260.785 253.46 254.355 1 2.37 ? C1 PLX 203 V 1 
HETATM 28 N N1 PLX . . . IB 47 259.898 254.61 254.063 1 2.22 ? N1 PLX 203 V 1 
HETATM 29 C C1C PLX . . . IB 47 259.131 255.217 255.147 1 2 ? C1C PLX 203 V 1 
HETATM 30 C C1B PLX . . . IB 47 258.961 254.187 253.039 1 2.26 ? C1B PLX 203 V 1 
HETATM 31 C C1A PLX . . . IB 47 260.757 255.656 253.544 1 2 ? C1A PLX 203 V 1 
HETATM 32 O O2 PLX . . . IB 47 260.028 249.622 256.46 1 19.56 ? O2 PLX 203 V 1 
HETATM 33 C C5 PLX . . . IB 47 264.216 249.011 253.553 1 33.4 ? C5 PLX 203 V 1 
HETATM 34 O O8 PLX . . . IB 47 264.091 248.891 252.124 1 37.15 ? O8 PLX 203 V 1 
HETATM 35 C C24 PLX . . . IB 47 264.101 250.133 251.461 1 38.76 ? C24 PLX 203 V 1 
HETATM 36 O O9 PLX . . . IB 47 262.981 250.867 251.851 1 38.8 ? O9 PLX 203 V 1 
HETATM 37 C C25 PLX . . . IB 47 264.043 249.919 249.954 1 38.96 ? C25 PLX 203 V 1 
HETATM 38 C C26 PLX . . . IB 47 263.45 251.142 249.237 1 38.45 ? C26 PLX 203 V 1 
HETATM 39 C C27 PLX . . . IB 47 264.166 251.422 247.894 1 37.88 ? C27 PLX 203 V 1 
HETATM 40 C C28 PLX . . . IB 47 265.118 252.638 247.961 1 37.56 ? C28 PLX 203 V 1 
HETATM 41 C C29 PLX . . . IB 47 266.383 252.438 247.107 1 40.01 ? C29 PLX 203 V 1 
HETATM 42 C C30 PLX . . . IB 47 266.092 252.387 245.599 1 42.17 ? C30 PLX 203 V 1 
HETATM 43 C C31 PLX . . . IB 47 267.367 252.168 244.779 1 43.78 ? C31 PLX 203 V 1 
HETATM 44 C C32 PLX . . . IB 47 267.121 251.425 243.453 1 45.48 ? C32 PLX 203 V 1 
HETATM 45 C C33 PLX . . . IB 47 266.833 249.93 243.658 1 46.77 ? C33 PLX 203 V 1 
HETATM 46 C C34 PLX . . . IB 47 267.47 249.039 242.569 1 48 ? C34 PLX 203 V 1 
HETATM 47 C C35 PLX . . . IB 47 266.463 248.538 241.532 1 46.66 ? C35 PLX 203 V 1 
HETATM 48 C C36 PLX . . . IB 47 267.141 248.257 240.179 1 44.97 ? C36 PLX 203 V 1 
HETATM 49 C C37 PLX . . . IB 47 267.921 249.471 239.657 1 42.83 ? C37 PLX 203 V 1 
HETATM 50 C C38 PLX . . . IB 47 269.065 249.086 238.715 1 40.79 ? C38 PLX 203 V 1 
HETATM 51 C C39 PLX . . . IB 47 269.732 250.319 238.096 1 38.57 ? C39 PLX 203 V 1 
HETATM 52 O O3 PLX . . . IB 47 261.931 250.286 257.894 1 15.39 ? O3 PLX 203 V 1 
#
_model_server_stats.io_time_ms              37 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    141 
_model_server_stats.query_time_ms           581 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           52 
#