data_5KLB
#
_model_server_result.job_id            eNlA65PIx0JdnUvb-4j6CA 
_model_server_result.datetime_utc      '2024-11-16 10:42:34' 
_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          5klb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"U","auth_seq_id":1303}' 
#
_entry.id    5KLB 
#
_exptl.entry_id    5KLB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              677.933 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE 
_entity.pdbx_number_of_molecules    20 
_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            5KLB 
_cell.length_a            124.9 
_cell.length_b            125.7 
_cell.length_c            191.485 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5KLB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 2 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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
? 2 E N N 
? 2 G N N 
? 2 L N N 
? 2 M N N 
? 2 N N N 
? 2 O N N 
? 2 P N N 
? 2 S N N 
? 2 T N N 
? 2 U N N 
? 2 V N N 
? 2 W N N 
? 2 X N N 
? 2 Y N N 
? 2 AA N N 
? 2 BA N N 
? 2 CA N N 
? 2 DA N N 
? 2 EA N N 
? 2 FA 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
metalc ? metalc1 HA O HOH . A HOH 1401 1_555 Z CA CA . D CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.872 ? 
metalc ? metalc2 B OD1 ASN 243 B ASN 1225 1_555 K CA CA . B CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.033 ? 
metalc ? metalc3 K CA CA . B CA 1301 1_555 C OE1 GLU 246 C GLU 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.097 ? 
metalc ? metalc4 K CA CA . B CA 1301 1_555 D OD1 ASN 243 D ASN 1225 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? 
metalc ? metalc5 K CA CA . B CA 1301 1_555 D OE1 GLU 246 D GLU 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.052 ? 
metalc ? metalc6 IA O HOH . B HOH 1401 1_555 Z CA CA . D CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.69 ? 
metalc ? metalc7 IA O HOH . B HOH 1404 1_555 Z CA CA . D CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.09 ? 
metalc ? metalc8 JA O HOH . C HOH 1401 1_555 Z CA CA . D CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.009 ? 
metalc ? metalc9 JA O HOH . C HOH 1402 1_555 Z CA CA . D CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.147 ? 
metalc ? metalc10 Z CA CA . D CA 1301 1_555 KA O HOH . D HOH 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.935 ? 
metalc ? metalc11 Z CA CA . D CA 1301 1_555 KA O HOH . D HOH 1403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? 
#
_chem_comp.formula           'C36 H72 N O8 P' 
_chem_comp.formula_weight    677.933 
_chem_comp.id                MC3 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1,2-DIMYRISTOYL-RAC-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
C1 C2 MC3 sing 308 n n 
C1 O3P MC3 sing 309 n n 
C1 H11 MC3 sing 310 n n 
C1 H12 MC3 sing 311 n n 
C2 C3 MC3 sing 312 n n 
C2 O2 MC3 sing 313 n n 
C2 H2 MC3 sing 314 n n 
C3 O3 MC3 sing 315 n n 
C3 H31 MC3 sing 316 n n 
C3 H32 MC3 sing 317 n n 
C4 C5 MC3 sing 318 n n 
C4 O4P MC3 sing 319 n n 
C4 H41 MC3 sing 320 n n 
C4 H42 MC3 sing 321 n n 
C5 N MC3 sing 322 n n 
C5 H51 MC3 sing 323 n n 
C5 H52 MC3 sing 324 n n 
C6 N MC3 sing 325 n n 
C6 H61 MC3 sing 326 n n 
C6 H62 MC3 sing 327 n n 
C6 H63 MC3 sing 328 n n 
C7 N MC3 sing 329 n n 
C7 H71 MC3 sing 330 n n 
C7 H72 MC3 sing 331 n n 
C7 H73 MC3 sing 332 n n 
C8 N MC3 sing 333 n n 
C8 H81 MC3 sing 334 n n 
C8 H82 MC3 sing 335 n n 
C8 H83 MC3 sing 336 n n 
C11 C12 MC3 sing 337 n n 
C11 O3 MC3 sing 338 n n 
C11 O11 MC3 doub 339 n n 
C12 C13 MC3 sing 340 n n 
C12 H121 MC3 sing 341 n n 
C12 H122 MC3 sing 342 n n 
C13 C14 MC3 sing 343 n n 
C13 H131 MC3 sing 344 n n 
C13 H132 MC3 sing 345 n n 
C14 C15 MC3 sing 346 n n 
C14 H141 MC3 sing 347 n n 
C14 H142 MC3 sing 348 n n 
C15 C16 MC3 sing 349 n n 
C15 H151 MC3 sing 350 n n 
C15 H152 MC3 sing 351 n n 
C16 C17 MC3 sing 352 n n 
C16 H161 MC3 sing 353 n n 
C16 H162 MC3 sing 354 n n 
C17 C18 MC3 sing 355 n n 
C17 H171 MC3 sing 356 n n 
C17 H172 MC3 sing 357 n n 
C18 C19 MC3 sing 358 n n 
C18 H181 MC3 sing 359 n n 
C18 H182 MC3 sing 360 n n 
C19 C20 MC3 sing 361 n n 
C19 H191 MC3 sing 362 n n 
C19 H192 MC3 sing 363 n n 
C20 C21 MC3 sing 364 n n 
C20 H201 MC3 sing 365 n n 
C20 H202 MC3 sing 366 n n 
C21 C22 MC3 sing 367 n n 
C21 H211 MC3 sing 368 n n 
C21 H212 MC3 sing 369 n n 
C22 C23 MC3 sing 370 n n 
C22 H221 MC3 sing 371 n n 
C22 H222 MC3 sing 372 n n 
C23 C24 MC3 sing 373 n n 
C23 H231 MC3 sing 374 n n 
C23 H232 MC3 sing 375 n n 
C24 H241 MC3 sing 376 n n 
C24 H242 MC3 sing 377 n n 
C24 H243 MC3 sing 378 n n 
C31 C32 MC3 sing 379 n n 
C31 O2 MC3 sing 380 n n 
C31 O31 MC3 doub 381 n n 
C32 C33 MC3 sing 382 n n 
C32 H321 MC3 sing 383 n n 
C32 H322 MC3 sing 384 n n 
C33 C34 MC3 sing 385 n n 
C33 H331 MC3 sing 386 n n 
C33 H332 MC3 sing 387 n n 
C34 C35 MC3 sing 388 n n 
C34 H341 MC3 sing 389 n n 
C34 H342 MC3 sing 390 n n 
C35 C36 MC3 sing 391 n n 
C35 H351 MC3 sing 392 n n 
C35 H352 MC3 sing 393 n n 
C36 C37 MC3 sing 394 n n 
C36 H361 MC3 sing 395 n n 
C36 H362 MC3 sing 396 n n 
C37 C38 MC3 sing 397 n n 
C37 H371 MC3 sing 398 n n 
C37 H372 MC3 sing 399 n n 
C38 C39 MC3 sing 400 n n 
C38 H381 MC3 sing 401 n n 
C38 H382 MC3 sing 402 n n 
C39 C40 MC3 sing 403 n n 
C39 H391 MC3 sing 404 n n 
C39 H392 MC3 sing 405 n n 
C40 C41 MC3 sing 406 n n 
C40 H401 MC3 sing 407 n n 
C40 H402 MC3 sing 408 n n 
C41 C42 MC3 sing 409 n n 
C41 H411 MC3 sing 410 n n 
C41 H412 MC3 sing 411 n n 
C42 C43 MC3 sing 412 n n 
C42 H421 MC3 sing 413 n n 
C42 H422 MC3 sing 414 n n 
C43 C44 MC3 sing 415 n n 
C43 H431 MC3 sing 416 n n 
C43 H432 MC3 sing 417 n n 
C44 H441 MC3 sing 418 n n 
C44 H442 MC3 sing 419 n n 
C44 H443 MC3 sing 420 n n 
O1P P MC3 doub 421 n n 
O2P P MC3 sing 422 n n 
O3P P MC3 sing 423 n n 
O4P P MC3 sing 424 n n 
#
_atom_sites.entry_id                     5KLB 
_atom_sites.fract_transf_matrix[1][1]    0.008006 
_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]    0.007955 
_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]    0.005222 
_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
E 2 MC3 A 1 1301 1301 MC3 PX4 . 
F 3 CA A 1 1302 1302 CA CA . 
G 2 MC3 A 1 1303 1305 MC3 PX4 . 
H 4 CPS A 1 1304 402 CPS CPS . 
I 4 CPS A 1 1305 403 CPS CPS . 
J 4 CPS A 1 1306 404 CPS CPS . 
K 3 CA B 1 1301 1 CA CA . 
L 2 MC3 B 1 1302 1301 MC3 PX4 . 
M 2 MC3 B 1 1303 1305 MC3 PX4 . 
N 2 MC3 B 1 1304 1306 MC3 PX4 . 
O 2 MC3 B 1 1305 1307 MC3 PX4 . 
P 2 MC3 B 1 1306 1306 MC3 PX4 . 
Q 4 CPS B 1 1307 406 CPS CPS . 
R 4 CPS B 1 1308 407 CPS CPS . 
S 2 MC3 C 1 1301 1301 MC3 PX4 . 
T 2 MC3 C 1 1302 1302 MC3 PX4 . 
U 2 MC3 C 1 1303 1303 MC3 PX4 . 
V 2 MC3 C 1 1304 1304 MC3 PX4 . 
W 2 MC3 C 1 1305 1305 MC3 PX4 . 
X 2 MC3 C 1 1306 1306 MC3 PX4 . 
Y 2 MC3 C 1 1307 1304 MC3 PX4 . 
Z 3 CA D 1 1301 1302 CA CA . 
AA 2 MC3 D 1 1302 1301 MC3 PX4 . 
BA 2 MC3 D 1 1303 1302 MC3 PX4 . 
CA 2 MC3 D 1 1304 1303 MC3 PX4 . 
DA 2 MC3 D 1 1305 1304 MC3 PX4 . 
EA 2 MC3 D 1 1306 1305 MC3 PX4 . 
FA 2 MC3 D 1 1307 1306 MC3 PX4 . 
GA 4 CPS D 1 1308 405 CPS CPS . 
HA 5 HOH A 1 1401 5 HOH HOH . 
HA 5 HOH A 2 1402 7 HOH HOH . 
HA 5 HOH A 3 1403 1 HOH HOH . 
IA 5 HOH B 1 1401 12 HOH HOH . 
IA 5 HOH B 2 1402 4 HOH HOH . 
IA 5 HOH B 3 1403 1407 HOH HOH . 
IA 5 HOH B 4 1404 10 HOH HOH . 
IA 5 HOH B 5 1405 1408 HOH HOH . 
IA 5 HOH B 6 1406 1407 HOH HOH . 
JA 5 HOH C 1 1401 9 HOH HOH . 
JA 5 HOH C 2 1402 8 HOH HOH . 
JA 5 HOH C 3 1403 2 HOH HOH . 
KA 5 HOH D 1 1401 6 HOH HOH . 
KA 5 HOH D 2 1402 1408 HOH HOH . 
KA 5 HOH D 3 1403 11 HOH HOH . 
KA 5 HOH D 4 1404 3 HOH HOH . 
KA 5 HOH D 5 1405 1408 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 C1 MC3 . . . U 2 67.118 53.445 206.079 1 58.29 ? C1 MC3 1303 C 1 
HETATM 2 C C2 MC3 . . . U 2 66.995 52.478 207.25 1 60.96 ? C2 MC3 1303 C 1 
HETATM 3 C C3 MC3 . . . U 2 66.606 51.087 206.75 1 58.36 ? C3 MC3 1303 C 1 
HETATM 4 C C4 MC3 . . . U 2 66.939 50.992 202.427 1 62.83 ? C4 MC3 1303 C 1 
HETATM 5 C C5 MC3 . . . U 2 65.709 50.546 201.604 1 68.99 ? C5 MC3 1303 C 1 
HETATM 6 C C6 MC3 . . . U 2 65.586 52.726 200.466 1 59.61 ? C6 MC3 1303 C 1 
HETATM 7 C C7 MC3 . . . U 2 67.071 51.038 199.722 1 59.71 ? C7 MC3 1303 C 1 
HETATM 8 C C8 MC3 . . . U 2 64.692 50.57 199.457 1 51.12 ? C8 MC3 1303 C 1 
HETATM 9 C C11 MC3 . . . U 2 66.114 49.649 208.64 1 53.73 ? C11 MC3 1303 C 1 
HETATM 10 C C12 MC3 . . . U 2 66.764 48.557 209.479 1 52.17 ? C12 MC3 1303 C 1 
HETATM 11 C C13 MC3 . . . U 2 65.935 48.236 210.744 1 53.01 ? C13 MC3 1303 C 1 
HETATM 12 C C14 MC3 . . . U 2 66.897 48.186 211.95 1 53.48 ? C14 MC3 1303 C 1 
HETATM 13 C C15 MC3 . . . U 2 66.717 46.973 212.884 1 49.83 ? C15 MC3 1303 C 1 
HETATM 14 C C16 MC3 . . . U 2 67.57 47.203 214.168 1 57.86 ? C16 MC3 1303 C 1 
HETATM 15 C C17 MC3 . . . U 2 67.128 46.38 215.409 1 56.52 ? C17 MC3 1303 C 1 
HETATM 16 C C18 MC3 . . . U 2 67.761 46.932 216.718 1 52.52 ? C18 MC3 1303 C 1 
HETATM 17 C C19 MC3 . . . U 2 67.774 45.831 217.812 1 54.74 ? C19 MC3 1303 C 1 
HETATM 18 C C20 MC3 . . . U 2 66.358 45.268 218.138 1 56.22 ? C20 MC3 1303 C 1 
HETATM 19 C C21 MC3 . . . U 2 66.137 45.171 219.684 1 58.57 ? C21 MC3 1303 C 1 
HETATM 20 C C31 MC3 . . . U 2 68.241 53.309 209.003 1 69.56 ? C31 MC3 1303 C 1 
HETATM 21 C C32 MC3 . . . U 2 69.136 52.756 210.121 1 67.04 ? C32 MC3 1303 C 1 
HETATM 22 C C33 MC3 . . . U 2 68.509 53.057 211.481 1 63.21 ? C33 MC3 1303 C 1 
HETATM 23 C C34 MC3 . . . U 2 67.97 51.781 212.152 1 65.46 ? C34 MC3 1303 C 1 
HETATM 24 C C35 MC3 . . . U 2 67.209 52.13 213.445 1 69.64 ? C35 MC3 1303 C 1 
HETATM 25 C C36 MC3 . . . U 2 68.169 52.394 214.626 1 63.55 ? C36 MC3 1303 C 1 
HETATM 26 C C37 MC3 . . . U 2 67.467 52.118 215.981 1 68.96 ? C37 MC3 1303 C 1 
HETATM 27 C C38 MC3 . . . U 2 66.389 51.001 215.862 1 72.67 ? C38 MC3 1303 C 1 
HETATM 28 C C39 MC3 . . . U 2 66.034 50.4 217.265 1 74.95 ? C39 MC3 1303 C 1 
HETATM 29 C C40 MC3 . . . U 2 64.506 50.162 217.465 1 72.12 ? C40 MC3 1303 C 1 
HETATM 30 C C41 MC3 . . . U 2 64.109 50.417 218.951 1 78.12 ? C41 MC3 1303 C 1 
HETATM 31 N N MC3 . . . U 2 65.72 51.253 200.286 1 65.49 ? N MC3 1303 C 1 
HETATM 32 O O2 MC3 . . . U 2 68.223 52.432 207.907 1 63.24 ? O2 MC3 1303 C 1 
HETATM 33 O O3 MC3 . . . U 2 67.049 50.148 207.717 1 59.99 ? O3 MC3 1303 C 1 
HETATM 34 O O11 MC3 . . . U 2 65.101 48.97 207.992 1 50.7 ? O11 MC3 1303 C 1 
HETATM 35 O O31 MC3 . . . U 2 68.704 54.567 208.597 1 71.09 ? O31 MC3 1303 C 1 
HETATM 36 O O1P MC3 . . . U 2 67.242 54.602 203.51 1 61.99 ? O1P MC3 1303 C 1 
HETATM 37 O O2P MC3 . . . U 2 68.966 52.971 202.726 1 61.01 ? O2P MC3 1303 C 1 
HETATM 38 O O3P MC3 . . . U 2 68.042 52.88 205.183 1 63.18 ? O3P MC3 1303 C 1 
HETATM 39 O O4P MC3 . . . U 2 66.552 52.129 203.166 1 59.21 ? O4P MC3 1303 C 1 
HETATM 40 P P MC3 . . . U 2 67.736 53.177 203.588 1 59.22 ? P MC3 1303 C 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    39 
_model_server_stats.query_time_ms           268 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           40 
#