data_6LKN
#
_model_server_result.job_id            29f4f7Z19l6z4kmeFL9Nww 
_model_server_result.datetime_utc      '2024-12-12 11:17:19' 
_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          6lkn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"GA","auth_seq_id":1201}' 
#
_entry.id    6LKN 
#
_exptl.entry_id    6LKN 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              792.075 
_entity.id                          3 
_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    7 
_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            6LKN 
_cell.length_a            100.46 
_cell.length_b            232.83 
_cell.length_c            492.89 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6LKN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    'P 2ac 2ab' 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
PISA dimeric 2 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,I,J,K,L,M,N,O,P,NA 1 1 
C,D,Q,R,S,T,U,V,W,X,OA 2 1 
E,F,Y,Z,AA,BA,CA,DA,EA,FA,PA 3 1 
G,H,GA,HA,IA,JA,KA,LA,MA,QA 4 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
? 3 I N N 
? 3 K N N 
? 3 Q N N 
? 3 R N N 
? 3 Y N N 
? 3 Z N N 
? 3 GA 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 B SG CYS 91 C CYS 91 1_555 B SG CYS 104 C CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf2 B SG CYS 94 C CYS 94 1_555 B SG CYS 102 C CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf3 C SG CYS 165 E CYS 165 1_555 C SG CYS 197 E CYS 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.787 ? 
disulf ? disulf4 D SG CYS 94 F CYS 94 1_555 D SG CYS 102 F CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf5 F SG CYS 91 J CYS 91 1_555 F SG CYS 104 J CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf6 F SG CYS 94 J CYS 94 1_555 F SG CYS 102 J CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf7 H SG CYS 91 N CYS 91 1_555 H SG CYS 104 N CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? 
disulf ? disulf8 H SG CYS 94 N CYS 94 1_555 H SG CYS 102 N CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
covale ? covale1 A C THR 408 A THR 408 1_555 A N BFD 409 A BFD 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale2 A C BFD 409 A BFD 409 1_555 A N LYS 410 A LYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale3 C C THR 408 E THR 408 1_555 C N BFD 409 E BFD 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
covale ? covale4 C C BFD 409 E BFD 409 1_555 C N LYS 410 E LYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale5 E C THR 408 I THR 408 1_555 E N BFD 409 I BFD 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale6 E C BFD 409 I BFD 409 1_555 E N LYS 410 I LYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale7 G C THR 408 M THR 408 1_555 G N BFD 409 M BFD 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale8 G C BFD 409 M BFD 409 1_555 G N LYS 410 M LYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
metalc ? metalc1 A OD2 BFD 409 A BFD 409 1_555 J MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.685 ? 
metalc ? metalc2 A OD1 ASP 816 A ASP 816 1_555 J MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.981 ? 
metalc ? metalc3 A OD1 ASP 820 A ASP 820 1_555 J MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.943 ? 
metalc ? metalc4 J MG MG . A MG 1202 1_555 NA O HOH . A HOH 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? 
metalc ? metalc5 J MG MG . A MG 1202 1_555 NA O HOH . A HOH 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? 
metalc ? metalc6 S MG MG . E MG 1203 1_555 OA O HOH . E HOH 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? 
metalc ? metalc7 S MG MG . E MG 1203 1_555 OA O HOH . E HOH 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? 
metalc ? metalc8 E O THR 411 I THR 411 1_555 AA MG MG . I MG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? 
metalc ? metalc9 E OD1 ASP 816 I ASP 816 1_555 AA MG MG . I MG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.865 ? 
metalc ? metalc10 AA MG MG . I MG 1203 1_555 PA O HOH . I HOH 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? 
metalc ? metalc11 AA MG MG . I MG 1203 1_555 PA O HOH . I HOH 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? 
metalc ? metalc12 G OG1 THR 413 M THR 413 1_555 HA MG MG . M MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.989 ? 
metalc ? metalc13 G OD2 ASP 816 M ASP 816 1_555 HA MG MG . M MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.809 ? 
metalc ? metalc14 HA MG MG . M MG 1202 1_555 QA O HOH . M HOH 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc15 HA MG MG . M MG 1202 1_555 QA O HOH . M HOH 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? 
#
_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 308 n n 
O C P5S doub 309 n n 
C OXT P5S sing 310 n n 
CA N P5S sing 311 n n 
N HN P5S sing 312 n n 
N HNA P5S sing 313 n n 
O19 C1 P5S sing 314 n n 
C1 C2 P5S sing 315 n n 
C1 H1 P5S sing 316 n n 
C1 H1A P5S sing 317 n n 
C2 O37 P5S sing 318 n n 
C2 C3 P5S sing 319 n n 
C2 H2 P5S sing 320 n n 
O16 C3 P5S sing 321 n n 
C3 H3 P5S sing 322 n n 
C3 H3A P5S sing 323 n n 
CB CA P5S sing 324 n n 
CA HA P5S sing 325 n n 
CB OG P5S sing 326 n n 
CB HB P5S sing 327 n n 
CB HBA P5S sing 328 n n 
P12 OG P5S sing 329 n n 
O16 P12 P5S sing 330 n n 
O13 P12 P5S doub 331 n n 
P12 O15 P5S sing 332 n n 
O15 HO15 P5S sing 333 n n 
C20 C17 P5S sing 334 n n 
O19 C17 P5S sing 335 n n 
C17 O18 P5S doub 336 n n 
C21 C20 P5S sing 337 n n 
C20 H20 P5S sing 338 n n 
C20 H20A P5S sing 339 n n 
C21 C22 P5S sing 340 n n 
C21 H21 P5S sing 341 n n 
C21 H21A P5S sing 342 n n 
C23 C22 P5S sing 343 n n 
C22 H22 P5S sing 344 n n 
C22 H22A P5S sing 345 n n 
C24 C23 P5S sing 346 n n 
C23 H23 P5S sing 347 n n 
C23 H23A P5S sing 348 n n 
C25 C24 P5S sing 349 n n 
C24 H24 P5S sing 350 n n 
C24 H24A P5S sing 351 n n 
C26 C25 P5S sing 352 n n 
C25 H25 P5S sing 353 n n 
C25 H25A P5S sing 354 n n 
C26 C27 P5S sing 355 n n 
C26 H26 P5S sing 356 n n 
C26 H26A P5S sing 357 n n 
C27 C28 P5S sing 358 n n 
C27 H27 P5S sing 359 n n 
C27 H27A P5S sing 360 n n 
C29 C28 P5S sing 361 n n 
C28 H28 P5S sing 362 n n 
C28 H28A P5S sing 363 n n 
C30 C29 P5S sing 364 n n 
C29 H29 P5S sing 365 n n 
C29 H29A P5S sing 366 n n 
C31 C30 P5S sing 367 n n 
C30 H30 P5S sing 368 n n 
C30 H30A P5S sing 369 n n 
C31 C32 P5S sing 370 n n 
C31 H31 P5S sing 371 n n 
C31 H31A P5S sing 372 n n 
C33 C32 P5S sing 373 n n 
C32 H32 P5S sing 374 n n 
C32 H32A P5S sing 375 n n 
C33 C34 P5S sing 376 n n 
C33 H33 P5S sing 377 n n 
C33 H33A P5S sing 378 n n 
C35 C34 P5S sing 379 n n 
C34 H34 P5S sing 380 n n 
C34 H34A P5S sing 381 n n 
C36 C35 P5S sing 382 n n 
C35 H35 P5S sing 383 n n 
C35 H35A P5S sing 384 n n 
C36 H36 P5S sing 385 n n 
C36 H36A P5S sing 386 n n 
C36 H36B P5S sing 387 n n 
C38 O37 P5S sing 388 n n 
O47 C38 P5S doub 389 n n 
C38 C39 P5S sing 390 n n 
C40 C39 P5S sing 391 n n 
C39 H39 P5S sing 392 n n 
C39 H39A P5S sing 393 n n 
C41 C40 P5S sing 394 n n 
C40 H40 P5S sing 395 n n 
C40 H40A P5S sing 396 n n 
C42 C41 P5S sing 397 n n 
C41 H41 P5S sing 398 n n 
C41 H41A P5S sing 399 n n 
C43 C42 P5S sing 400 n n 
C42 H42 P5S sing 401 n n 
C42 H42A P5S sing 402 n n 
C43 C44 P5S sing 403 n n 
C43 H43 P5S sing 404 n n 
C43 H43A P5S sing 405 n n 
C44 C45 P5S sing 406 n n 
C44 H44 P5S sing 407 n n 
C44 H44A P5S sing 408 n n 
C45 C46 P5S sing 409 n n 
C45 H45 P5S sing 410 n n 
C45 H45A P5S sing 411 n n 
C46 C48 P5S sing 412 n n 
C46 H46 P5S sing 413 n n 
C46 H46A P5S sing 414 n n 
C48 C49 P5S sing 415 n n 
C48 H48 P5S sing 416 n n 
C48 H48A P5S sing 417 n n 
C49 C50 P5S sing 418 n n 
C49 H49 P5S sing 419 n n 
C49 H49A P5S sing 420 n n 
C50 C51 P5S sing 421 n n 
C50 H50 P5S sing 422 n n 
C50 H50A P5S sing 423 n n 
C51 C52 P5S sing 424 n n 
C51 H51 P5S sing 425 n n 
C51 H51A P5S sing 426 n n 
C53 C52 P5S sing 427 n n 
C52 H52 P5S sing 428 n n 
C52 H52A P5S sing 429 n n 
C53 C54 P5S sing 430 n n 
C53 H53 P5S sing 431 n n 
C53 H53A P5S sing 432 n n 
C55 C54 P5S sing 433 n n 
C54 H54 P5S sing 434 n n 
C54 H54A P5S sing 435 n n 
C55 C56 P5S sing 436 n n 
C55 H55 P5S sing 437 n n 
C55 H55A P5S sing 438 n n 
C56 H56 P5S sing 439 n n 
C56 H56A P5S sing 440 n n 
C56 H56B P5S sing 441 n n 
OXT HXT P5S sing 442 n n 
#
_atom_sites.entry_id                     6LKN 
_atom_sites.fract_transf_matrix[1][1]    0.009954 
_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]    0.004295 
_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]    0.002029 
_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
I 3 P5S A 1 1201 2000 P5S P5S . 
J 4 MG A 1 1202 2002 MG MO6 . 
K 3 P5S C 1 401 1999 P5S P5S . 
L 5 NAG C 1 402 401 NAG NAG . 
M 5 NAG C 1 403 402 NAG NAG . 
N 6 AH2 C 1 404 403 AH2 MAN . 
O 5 NAG C 1 405 404 NAG NAG . 
P 5 NAG C 1 406 405 NAG NAG . 
Q 3 P5S E 1 1201 1999 P5S P5S . 
R 3 P5S E 1 1202 2000 P5S P5S . 
S 4 MG E 1 1203 2002 MG MO6 . 
T 5 NAG F 1 401 401 NAG NAG . 
U 5 NAG F 1 402 402 NAG NAG . 
V 6 AH2 F 1 403 403 AH2 MAN . 
W 5 NAG F 1 404 404 NAG NAG . 
X 5 NAG F 1 405 405 NAG NAG . 
Y 3 P5S I 1 1201 1999 P5S P5S . 
Z 3 P5S I 1 1202 2000 P5S P5S . 
AA 4 MG I 1 1203 2002 MG MO6 . 
BA 5 NAG J 1 401 401 NAG NAG . 
CA 5 NAG J 1 402 402 NAG NAG . 
DA 6 AH2 J 1 403 403 AH2 MAN . 
EA 5 NAG J 1 404 404 NAG NAG . 
FA 5 NAG J 1 405 405 NAG NAG . 
GA 3 P5S M 1 1201 1999 P5S P5S . 
HA 4 MG M 1 1202 2002 MG MO6 . 
IA 5 NAG N 1 401 401 NAG NAG . 
JA 5 NAG N 1 402 402 NAG NAG . 
KA 6 AH2 N 1 403 403 AH2 MAN . 
LA 5 NAG N 1 404 404 NAG NAG . 
MA 5 NAG N 1 405 405 NAG NAG . 
NA 7 HOH A 1 1301 2002 HOH MO6 . 
NA 7 HOH A 2 1302 2002 HOH MO6 . 
OA 7 HOH E 1 1301 2002 HOH MO6 . 
OA 7 HOH E 2 1302 2002 HOH MO6 . 
PA 7 HOH I 1 1301 2002 HOH MO6 . 
PA 7 HOH I 2 1302 2002 HOH MO6 . 
QA 7 HOH M 1 1301 2002 HOH MO6 . 
QA 7 HOH M 2 1302 2002 HOH MO6 . 
#
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 . . . GA 3 22.154 59.075 -215.275 1 298.31 ? C P5S 1201 M 1 
HETATM 2 N N P5S . . . GA 3 21.734 59.375 -212.891 1 293.39 ? N P5S 1201 M 1 
HETATM 3 O O P5S . . . GA 3 23.36 59.209 -215.387 1 299.03 ? O P5S 1201 M 1 
HETATM 4 C CA P5S . . . GA 3 21.402 59.861 -214.244 1 296.65 ? CA P5S 1201 M 1 
HETATM 5 C CB P5S . . . GA 3 21.737 61.34 -214.384 1 300.25 ? CB P5S 1201 M 1 
HETATM 6 O OG P5S . . . GA 3 21.073 62.094 -213.374 1 303.28 ? OG P5S 1201 M 1 
HETATM 7 P P12 P5S . . . GA 3 21.393 63.665 -213.232 1 309.44 ? P12 P5S 1201 M 1 
HETATM 8 O O13 P5S . . . GA 3 22.842 63.842 -212.993 1 310.9 ? O13 P5S 1201 M 1 
HETATM 9 O O15 P5S . . . GA 3 20.984 64.426 -214.59 1 312.01 ? O15 P5S 1201 M 1 
HETATM 10 O O16 P5S . . . GA 3 20.559 64.274 -211.997 1 308.23 ? O16 P5S 1201 M 1 
HETATM 11 O OXT P5S . . . GA 3 21.516 58.226 -216.074 1 299.28 ? OXT P5S 1201 M 1 
#
_model_server_stats.io_time_ms              90 
_model_server_stats.parse_time_ms           29 
_model_server_stats.create_model_time_ms    300 
_model_server_stats.query_time_ms           233 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           11 
#