data_6XVF
#
_model_server_result.job_id            1I6DoZ5-ZseEoxW7qDKSKA 
_model_server_result.datetime_utc      '2024-11-05 04:54:56' 
_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          6xvf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"CA","auth_seq_id":202}' 
#
_entry.id    6XVF 
#
_exptl.entry_id    6XVF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              678.94 
_entity.id                          21 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE 
_entity.pdbx_number_of_molecules    1 
_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         120 
_cell.entry_id            6XVF 
_cell.length_a            209.869 
_cell.length_b            209.869 
_cell.length_c            342.418 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6XVF 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        179 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    eicosameric 
_pdbx_struct_assembly.oligomeric_count      20 
_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,LA,MA,NA,OA,PA,QA,RA 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 10_445 -y-1,-x-1,-z+1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 -104.9345 -181.751885 57.069667 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      21 
_struct_asym.id                             CA 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 E SG CYS 144 E CYS 144 1_555 E SG CYS 160 E CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf2 H SG CYS 11 H CYS 24 1_555 H SG CYS 55 H CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf3 H SG CYS 27 H CYS 40 1_555 H SG CYS 41 H CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
metalc ? metalc1 C NE2 HIS 82 C HIS 83 1_555 P FE HEM . C HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? 
metalc ? metalc2 C NE2 HIS 96 C HIS 97 1_555 Q FE HEM . C HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? 
metalc ? metalc3 C NE2 HIS 181 C HIS 182 1_555 P FE HEM . C HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? 
metalc ? metalc4 C NE2 HIS 195 C HIS 196 1_555 Q FE HEM . C HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? 
metalc ? metalc5 D NE2 HIS 40 D HIS 41 1_555 Y FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? 
metalc ? metalc6 D SD MET 159 D MET 160 1_555 Y FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? 
metalc ? metalc7 E SG CYS 158 E CYS 158 1_555 BA FE1 FES . E FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? 
#
_chem_comp.formula           'C36 H73 N O8 P 1' 
_chem_comp.formula_weight    678.94 
_chem_comp.id                PX4 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
O1 P1 PX4 sing 1058 n n 
O1 H1P PX4 sing 1059 n n 
O2 P1 PX4 doub 1060 n n 
P1 O3 PX4 sing 1061 n n 
P1 O4 PX4 sing 1062 n n 
O3 C1 PX4 sing 1063 n n 
C1 C2 PX4 sing 1064 n n 
C1 H1 PX4 sing 1065 n n 
C1 H2 PX4 sing 1066 n n 
C2 N1 PX4 sing 1067 n n 
C2 H3 PX4 sing 1068 n n 
C2 H4 PX4 sing 1069 n n 
N1 C3 PX4 sing 1070 n n 
N1 C4 PX4 sing 1071 n n 
N1 C5 PX4 sing 1072 n n 
C3 H5 PX4 sing 1073 n n 
C3 H6 PX4 sing 1074 n n 
C3 H7 PX4 sing 1075 n n 
C4 H8 PX4 sing 1076 n n 
C4 H9 PX4 sing 1077 n n 
C4 H10 PX4 sing 1078 n n 
C5 H11 PX4 sing 1079 n n 
C5 H12 PX4 sing 1080 n n 
C5 H13 PX4 sing 1081 n n 
O4 C6 PX4 sing 1082 n n 
C6 C7 PX4 sing 1083 n n 
C6 H14 PX4 sing 1084 n n 
C6 H15 PX4 sing 1085 n n 
C7 C8 PX4 sing 1086 n n 
C7 O7 PX4 sing 1087 n n 
C7 H16 PX4 sing 1088 n n 
C8 O5 PX4 sing 1089 n n 
C8 H17 PX4 sing 1090 n n 
C8 H18 PX4 sing 1091 n n 
O5 C9 PX4 sing 1092 n n 
C9 O6 PX4 doub 1093 n n 
C9 C10 PX4 sing 1094 n n 
C10 C11 PX4 sing 1095 n n 
C10 H19 PX4 sing 1096 n n 
C10 H20 PX4 sing 1097 n n 
C11 C12 PX4 sing 1098 n n 
C11 H21 PX4 sing 1099 n n 
C11 H22 PX4 sing 1100 n n 
C12 C13 PX4 sing 1101 n n 
C12 H23 PX4 sing 1102 n n 
C12 H24 PX4 sing 1103 n n 
C13 C14 PX4 sing 1104 n n 
C13 H25 PX4 sing 1105 n n 
C13 H26 PX4 sing 1106 n n 
C14 C15 PX4 sing 1107 n n 
C14 H27 PX4 sing 1108 n n 
C14 H28 PX4 sing 1109 n n 
C15 C16 PX4 sing 1110 n n 
C15 H29 PX4 sing 1111 n n 
C15 H30 PX4 sing 1112 n n 
C16 C17 PX4 sing 1113 n n 
C16 H31 PX4 sing 1114 n n 
C16 H32 PX4 sing 1115 n n 
C17 C18 PX4 sing 1116 n n 
C17 H33 PX4 sing 1117 n n 
C17 H34 PX4 sing 1118 n n 
C18 C19 PX4 sing 1119 n n 
C18 H35 PX4 sing 1120 n n 
C18 H36 PX4 sing 1121 n n 
C19 C20 PX4 sing 1122 n n 
C19 H37 PX4 sing 1123 n n 
C19 H38 PX4 sing 1124 n n 
C20 C21 PX4 sing 1125 n n 
C20 H39 PX4 sing 1126 n n 
C20 H40 PX4 sing 1127 n n 
C21 C22 PX4 sing 1128 n n 
C21 H41 PX4 sing 1129 n n 
C21 H42 PX4 sing 1130 n n 
C22 H43 PX4 sing 1131 n n 
C22 H44 PX4 sing 1132 n n 
C22 H45 PX4 sing 1133 n n 
O7 C23 PX4 sing 1134 n n 
C23 O8 PX4 doub 1135 n n 
C23 C24 PX4 sing 1136 n n 
C24 C25 PX4 sing 1137 n n 
C24 H46 PX4 sing 1138 n n 
C24 H47 PX4 sing 1139 n n 
C25 C26 PX4 sing 1140 n n 
C25 H48 PX4 sing 1141 n n 
C25 H49 PX4 sing 1142 n n 
C26 C27 PX4 sing 1143 n n 
C26 H50 PX4 sing 1144 n n 
C26 H51 PX4 sing 1145 n n 
C27 C28 PX4 sing 1146 n n 
C27 H52 PX4 sing 1147 n n 
C27 H53 PX4 sing 1148 n n 
C28 C29 PX4 sing 1149 n n 
C28 H54 PX4 sing 1150 n n 
C28 H55 PX4 sing 1151 n n 
C29 C30 PX4 sing 1152 n n 
C29 H56 PX4 sing 1153 n n 
C29 H57 PX4 sing 1154 n n 
C30 C31 PX4 sing 1155 n n 
C30 H58 PX4 sing 1156 n n 
C30 H59 PX4 sing 1157 n n 
C31 C32 PX4 sing 1158 n n 
C31 H60 PX4 sing 1159 n n 
C31 H61 PX4 sing 1160 n n 
C32 C33 PX4 sing 1161 n n 
C32 H62 PX4 sing 1162 n n 
C32 H63 PX4 sing 1163 n n 
C33 C34 PX4 sing 1164 n n 
C33 H64 PX4 sing 1165 n n 
C33 H65 PX4 sing 1166 n n 
C34 C35 PX4 sing 1167 n n 
C34 H66 PX4 sing 1168 n n 
C34 H67 PX4 sing 1169 n n 
C35 C36 PX4 sing 1170 n n 
C35 H68 PX4 sing 1171 n n 
C35 H69 PX4 sing 1172 n n 
C36 H70 PX4 sing 1173 n n 
C36 H71 PX4 sing 1174 n n 
C36 H72 PX4 sing 1175 n n 
#
_atom_sites.entry_id                     6XVF 
_atom_sites.fract_transf_matrix[1][1]    0.004765 
_atom_sites.fract_transf_matrix[1][2]    0.002751 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.005502 
_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]    0.00292 
_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
K 11 PG4 A 1 501 501 PG4 PG4 . 
L 12 6PE A 1 502 502 6PE 6PE . 
M 13 PO4 A 1 503 503 PO4 PO4 . 
N 14 CDL A 1 504 401 CDL CDL . 
O 13 PO4 B 1 501 501 PO4 PO4 . 
P 15 HEM C 1 401 402 HEM HEM . 
Q 15 HEM C 1 402 403 HEM HEM . 
R 16 LMT C 1 403 405 LMT LMT . 
S 11 PG4 C 1 404 406 PG4 PG4 . 
T 11 PG4 C 1 405 407 PG4 PG4 . 
U 14 CDL C 1 406 408 CDL CDL . 
V 17 PEE C 1 407 409 PEE PEE . 
W 18 JAG C 1 408 404 JAG JAG . 
X 13 PO4 C 1 409 410 PO4 PO4 . 
Y 19 HEC D 1 501 501 HEC HEC . 
Z 13 PO4 D 1 502 502 PO4 PO4 . 
AA 14 CDL D 1 503 503 CDL CDL . 
BA 20 FES E 1 201 201 FES FES . 
CA 21 PX4 E 1 202 202 PX4 PX4 . 
DA 13 PO4 E 1 203 203 PO4 PO4 . 
EA 17 PEE E 1 204 204 PEE PEE . 
FA 14 CDL E 1 205 205 CDL CDL . 
GA 13 PO4 F 1 501 501 PO4 PO4 . 
HA 13 PO4 G 1 101 101 PO4 PO4 . 
IA 13 PO4 G 1 102 102 PO4 PO4 . 
JA 13 PO4 G 1 103 103 PO4 PO4 . 
KA 22 HOH A 1 601 504 HOH HOH . 
KA 22 HOH A 2 602 508 HOH HOH . 
KA 22 HOH A 3 603 507 HOH HOH . 
KA 22 HOH A 4 604 505 HOH HOH . 
KA 22 HOH A 5 605 509 HOH HOH . 
KA 22 HOH A 6 606 506 HOH HOH . 
LA 22 HOH B 1 601 502 HOH HOH . 
LA 22 HOH B 2 602 503 HOH HOH . 
MA 22 HOH C 1 501 412 HOH HOH . 
MA 22 HOH C 2 502 414 HOH HOH . 
MA 22 HOH C 3 503 411 HOH HOH . 
MA 22 HOH C 4 504 413 HOH HOH . 
NA 22 HOH D 1 601 505 HOH HOH . 
NA 22 HOH D 2 602 504 HOH HOH . 
OA 22 HOH F 1 601 502 HOH HOH . 
PA 22 HOH G 1 201 104 HOH HOH . 
QA 22 HOH I 1 101 101 HOH HOH . 
QA 22 HOH I 2 102 102 HOH HOH . 
RA 22 HOH J 1 101 101 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 O1 PX4 . . . CA 21 -67.1 -53.475 13.476 1 186.12 -1 O1 PX4 202 E 1 
HETATM 2 O O2 PX4 . . . CA 21 -65.13 -52.077 12.545 1 178.51 ? O2 PX4 202 E 1 
HETATM 3 P P1 PX4 . . . CA 21 -65.984 -53.324 12.469 1 183.28 ? P1 PX4 202 E 1 
HETATM 4 O O3 PX4 . . . CA 21 -66.616 -53.5 10.989 1 181.7 ? O3 PX4 202 E 1 
HETATM 5 C C1 PX4 . . . CA 21 -66.228 -52.76 9.83 1 178.26 ? C1 PX4 202 E 1 
HETATM 6 C C2 PX4 . . . CA 21 -67.502 -52.421 9.041 1 177.6 ? C2 PX4 202 E 1 
HETATM 7 N N1 PX4 . . . CA 21 -67.369 -51.85 7.68 1 176.63 ? N1 PX4 202 E 1 
HETATM 8 C C3 PX4 . . . CA 21 -68.6 -52.104 6.923 1 178.05 ? C3 PX4 202 E 1 
HETATM 9 C C4 PX4 . . . CA 21 -67.23 -50.398 7.723 1 175 ? C4 PX4 202 E 1 
HETATM 10 C C5 PX4 . . . CA 21 -66.259 -52.443 6.93 1 176.69 ? C5 PX4 202 E 1 
HETATM 11 O O4 PX4 . . . CA 21 -65.047 -54.648 12.577 1 184.94 ? O4 PX4 202 E 1 
HETATM 12 C C6 PX4 . . . CA 21 -65.436 -55.916 13.154 1 182.14 ? C6 PX4 202 E 1 
HETATM 13 C C7 PX4 . . . CA 21 -64.279 -56.938 13.297 1 181.63 ? C7 PX4 202 E 1 
HETATM 14 C C8 PX4 . . . CA 21 -63.763 -57.443 11.939 1 182.19 ? C8 PX4 202 E 1 
HETATM 15 O O5 PX4 . . . CA 21 -64.743 -58.101 11.128 1 182.84 ? O5 PX4 202 E 1 
HETATM 16 C C9 PX4 . . . CA 21 -64.736 -57.984 9.665 1 181.44 ? C9 PX4 202 E 1 
HETATM 17 O O6 PX4 . . . CA 21 -65.33 -57.036 9.156 1 182.68 ? O6 PX4 202 E 1 
HETATM 18 C C10 PX4 . . . CA 21 -64.066 -59.036 8.787 1 177.74 ? C10 PX4 202 E 1 
HETATM 19 C C11 PX4 . . . CA 21 -62.554 -58.891 8.598 1 173.23 ? C11 PX4 202 E 1 
HETATM 20 C C12 PX4 . . . CA 21 -61.825 -60.219 8.837 1 171.44 ? C12 PX4 202 E 1 
HETATM 21 C C13 PX4 . . . CA 21 -61.028 -60.714 7.628 1 171.73 ? C13 PX4 202 E 1 
HETATM 22 C C14 PX4 . . . CA 21 -60.062 -61.845 7.985 1 171.69 ? C14 PX4 202 E 1 
HETATM 23 C C15 PX4 . . . CA 21 -60.588 -63.205 7.513 1 174.12 ? C15 PX4 202 E 1 
HETATM 24 C C16 PX4 . . . CA 21 -60.214 -64.354 8.459 1 173.82 ? C16 PX4 202 E 1 
HETATM 25 C C17 PX4 . . . CA 21 -61.106 -65.598 8.311 1 172.24 ? C17 PX4 202 E 1 
HETATM 26 C C18 PX4 . . . CA 21 -60.565 -66.82 9.075 1 169.43 ? C18 PX4 202 E 1 
HETATM 27 C C19 PX4 . . . CA 21 -60.42 -68.08 8.204 1 168.02 ? C19 PX4 202 E 1 
HETATM 28 C C20 PX4 . . . CA 21 -59.104 -68.852 8.413 1 164.92 ? C20 PX4 202 E 1 
HETATM 29 C C21 PX4 . . . CA 21 -58.51 -69.428 7.12 1 162.52 ? C21 PX4 202 E 1 
HETATM 30 C C22 PX4 . . . CA 21 -57.769 -70.737 7.344 1 159.52 ? C22 PX4 202 E 1 
HETATM 31 O O7 PX4 . . . CA 21 -63.144 -56.362 13.977 1 179.96 ? O7 PX4 202 E 1 
HETATM 32 C C23 PX4 . . . CA 21 -62.62 -57.025 15.177 1 174.3 ? C23 PX4 202 E 1 
HETATM 33 O O8 PX4 . . . CA 21 -63.151 -56.747 16.25 1 175.62 ? O8 PX4 202 E 1 
HETATM 34 C C24 PX4 . . . CA 21 -61.45 -58.008 15.094 1 167.25 ? C24 PX4 202 E 1 
HETATM 35 C C25 PX4 . . . CA 21 -60.168 -57.552 15.808 1 160.78 ? C25 PX4 202 E 1 
HETATM 36 C C26 PX4 . . . CA 21 -60.224 -57.697 17.331 1 157.82 ? C26 PX4 202 E 1 
HETATM 37 C C27 PX4 . . . CA 21 -59.195 -58.668 17.896 1 155.36 ? C27 PX4 202 E 1 
#
_model_server_stats.io_time_ms              37 
_model_server_stats.parse_time_ms           23 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           339 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           37 
#