data_4K5Y
#
_model_server_result.job_id            6uFBIz4YNC2saw1aJCbMig 
_model_server_result.datetime_utc      '2024-11-14 12:57:25' 
_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          4k5y 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":502}' 
#
_entry.id    4K5Y 
#
_exptl.entry_id    4K5Y 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              749.007 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate' 
_entity.pdbx_number_of_molecules    3 
_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            4K5Y 
_cell.length_a            86.559 
_cell.length_b            123.968 
_cell.length_c            166.834 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4K5Y 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 2 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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,F,G,H,T 1 1 
B,I,J,K,L,M,N,O,P,Q,U 2 1 
C,R,S 3 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
? 6 K N N 
? 6 L N N 
? 6 M 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 A SG CYS 86 A CYS 188 1_555 A SG CYS 313 A CYS 258 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
disulf ? disulf2 B SG CYS 86 B CYS 188 1_555 B SG CYS 313 B CYS 258 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? 
disulf ? disulf3 C SG CYS 86 C CYS 188 1_555 C SG CYS 313 C CYS 258 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? 
#
_chem_comp.formula           'C40 H77 O10 P' 
_chem_comp.formula_weight    749.007 
_chem_comp.id                PGW 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Phospho-(1-glycerol)];PHOSPHATIDYLGLYCEROL 
#
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
CAD C05 PGW sing 446 n n 
CAD HAD PGW sing 447 n n 
CAD HADA PGW sing 448 n n 
OAE CAD PGW sing 449 n n 
OAE HOAE PGW sing 450 n n 
OAF C05 PGW sing 451 n n 
OAF HOAF PGW sing 452 n n 
P O13 PGW sing 453 n n 
P O11 PGW sing 454 n n 
C01 O03 PGW sing 455 n n 
C01 C02 PGW sing 456 n n 
C01 H01 PGW sing 457 n n 
C01 H01A PGW sing 458 n n 
C1 C2 PGW sing 459 n n 
O01 C1 PGW sing 460 n n 
C02 O01 PGW sing 461 n n 
C02 H02 PGW sing 462 n n 
C2 C3 PGW sing 463 n n 
C2 H2 PGW sing 464 n n 
C2 H2A PGW sing 465 n n 
O02 C1 PGW doub 466 n n 
C03 C02 PGW sing 467 n n 
C03 H03 PGW sing 468 n n 
C03 H03A PGW sing 469 n n 
C3 C4 PGW sing 470 n n 
C3 H3 PGW sing 471 n n 
C3 H3A PGW sing 472 n n 
C04 C05 PGW sing 473 n n 
C04 O12 PGW sing 474 n n 
C04 H04 PGW sing 475 n n 
C04 H04A PGW sing 476 n n 
C4 C5 PGW sing 477 n n 
C4 H4 PGW sing 478 n n 
C4 H4A PGW sing 479 n n 
O04 C19 PGW doub 480 n n 
C05 H05 PGW sing 481 n n 
C5 C6 PGW sing 482 n n 
C5 H5 PGW sing 483 n n 
C5 H5A PGW sing 484 n n 
C06 C07 PGW sing 485 n n 
C06 H06 PGW sing 486 n n 
C06 H06A PGW sing 487 n n 
C6 C7 PGW sing 488 n n 
C6 H6 PGW sing 489 n n 
C6 H6A PGW sing 490 n n 
C07 H07 PGW sing 491 n n 
C07 H07A PGW sing 492 n n 
C7 C8 PGW sing 493 n n 
C7 H7 PGW sing 494 n n 
C7 H7A PGW sing 495 n n 
C08 C07 PGW sing 496 n n 
C08 H08 PGW sing 497 n n 
C08 H08A PGW sing 498 n n 
C8 C9 PGW sing 499 n n 
C8 H8 PGW sing 500 n n 
C8 H8A PGW sing 501 n n 
C09 C08 PGW sing 502 n n 
C09 C11 PGW sing 503 n n 
C09 H09 PGW sing 504 n n 
C09 H09A PGW sing 505 n n 
C9 C10 PGW doub 506 z n 
C10 C06 PGW sing 507 n n 
C11 H11 PGW sing 508 n n 
C11 H11A PGW sing 509 n n 
O11 C03 PGW sing 510 n n 
C12 C11 PGW sing 511 n n 
C12 H12 PGW sing 512 n n 
C12 H12A PGW sing 513 n n 
O12 P PGW sing 514 n n 
C13 C12 PGW sing 515 n n 
C13 C14 PGW sing 516 n n 
C13 H13 PGW sing 517 n n 
C13 H13A PGW sing 518 n n 
O13 HO13 PGW sing 519 n n 
C14 H14 PGW sing 520 n n 
C14 H14A PGW sing 521 n n 
C14 H14B PGW sing 522 n n 
O14 P PGW doub 523 n n 
C15 C16 PGW sing 524 n n 
C15 H15 PGW sing 525 n n 
C15 H15A PGW sing 526 n n 
C16 H16 PGW sing 527 n n 
C16 H16A PGW sing 528 n n 
C17 C16 PGW sing 529 n n 
C17 C18 PGW sing 530 n n 
C17 H17 PGW sing 531 n n 
C17 H17A PGW sing 532 n n 
C18 C28 PGW sing 533 n n 
C18 H18 PGW sing 534 n n 
C18 H18A PGW sing 535 n n 
C19 O03 PGW sing 536 n n 
C19 C20 PGW sing 537 n n 
C20 C21 PGW sing 538 n n 
C20 H20 PGW sing 539 n n 
C20 H20A PGW sing 540 n n 
C21 C22 PGW sing 541 n n 
C21 H21 PGW sing 542 n n 
C21 H21A PGW sing 543 n n 
C22 C23 PGW sing 544 n n 
C22 H22 PGW sing 545 n n 
C22 H22A PGW sing 546 n n 
C23 C24 PGW sing 547 n n 
C23 H23 PGW sing 548 n n 
C23 H23A PGW sing 549 n n 
C24 C25 PGW sing 550 n n 
C24 H24 PGW sing 551 n n 
C24 H24A PGW sing 552 n n 
C25 C26 PGW sing 553 n n 
C25 H25 PGW sing 554 n n 
C25 H25A PGW sing 555 n n 
C26 C27 PGW sing 556 n n 
C26 H26 PGW sing 557 n n 
C26 H26A PGW sing 558 n n 
C27 C15 PGW sing 559 n n 
C27 H27 PGW sing 560 n n 
C27 H27A PGW sing 561 n n 
C28 H28 PGW sing 562 n n 
C28 H28A PGW sing 563 n n 
C29 H29 PGW sing 564 n n 
C29 H29A PGW sing 565 n n 
C29 H29B PGW sing 566 n n 
C30 C28 PGW sing 567 n n 
C30 C29 PGW sing 568 n n 
C30 H30 PGW sing 569 n n 
C30 H30A PGW sing 570 n n 
C9 H9 PGW sing 571 n n 
C10 H10 PGW sing 572 n n 
#
_atom_sites.entry_id                     4K5Y 
_atom_sites.fract_transf_matrix[1][1]    0.011553 
_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]    0.008067 
_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]    0.005994 
_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
D 2 1Q5 A 1 401 401 1Q5 1Q5 . 
E 3 OLA A 1 501 501 OLA OLA . 
F 4 OLC A 1 502 502 OLC OLC . 
G 4 OLC A 1 503 503 OLC OLC . 
H 5 SO4 A 1 504 504 SO4 SO4 . 
I 2 1Q5 B 1 401 401 1Q5 1Q5 . 
J 4 OLC B 1 501 501 OLC OLC . 
K 6 PGW B 1 502 502 PGW PGW . 
L 6 PGW B 1 503 503 PGW PGW . 
M 6 PGW B 1 504 504 PGW PGW . 
N 7 1PE B 1 505 505 1PE 1PE . 
O 5 SO4 B 1 506 506 SO4 SO4 . 
P 5 SO4 B 1 507 507 SO4 SO4 . 
Q 5 SO4 B 1 508 508 SO4 SO4 . 
R 2 1Q5 C 1 401 401 1Q5 1Q5 . 
S 3 OLA C 1 501 501 OLA OLA . 
T 8 HOH A 1 601 601 HOH HOH . 
T 8 HOH A 2 602 602 HOH HOH . 
T 8 HOH A 3 603 603 HOH HOH . 
T 8 HOH A 4 604 604 HOH HOH . 
U 8 HOH B 1 601 601 HOH HOH . 
U 8 HOH B 2 602 602 HOH HOH . 
U 8 HOH B 3 603 603 HOH HOH . 
U 8 HOH B 4 604 604 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 P P PGW . . . K 6 -57.498 16.453 27.468 1 114.62 ? P PGW 502 B 1 
HETATM 2 C C01 PGW . . . K 6 -53.095 16.347 26.356 1 58 ? C01 PGW 502 B 1 
HETATM 3 C C1 PGW . . . K 6 -53.283 19.796 25.338 1 54.74 ? C1 PGW 502 B 1 
HETATM 4 O O01 PGW . . . K 6 -53.409 18.555 25.195 1 70.34 ? O01 PGW 502 B 1 
HETATM 5 C C02 PGW . . . K 6 -53.872 17.664 26.313 1 64.05 ? C02 PGW 502 B 1 
HETATM 6 C C2 PGW . . . K 6 -51.908 20.395 25.514 1 46.29 ? C2 PGW 502 B 1 
HETATM 7 O O02 PGW . . . K 6 -54.235 20.552 25.036 1 44.47 ? O02 PGW 502 B 1 
HETATM 8 C C03 PGW . . . K 6 -55.363 17.37 26.122 1 63.43 ? C03 PGW 502 B 1 
HETATM 9 C C3 PGW . . . K 6 -50.819 19.394 25.116 1 42.69 ? C3 PGW 502 B 1 
HETATM 10 O O03 PGW . . . K 6 -52.379 16.095 27.648 1 66.81 ? O03 PGW 502 B 1 
HETATM 11 C C4 PGW . . . K 6 -49.748 19.384 26.211 1 47.03 ? C4 PGW 502 B 1 
HETATM 12 O O04 PGW . . . K 6 -51.485 14.254 28.374 1 73.24 ? O04 PGW 502 B 1 
HETATM 13 C C5 PGW . . . K 6 -48.452 18.752 25.699 1 55.85 ? C5 PGW 502 B 1 
HETATM 14 C C06 PGW . . . K 6 -45.173 23.62 25.454 1 49.66 ? C06 PGW 502 B 1 
HETATM 15 C C6 PGW . . . K 6 -47.374 18.874 26.782 1 52.55 ? C6 PGW 502 B 1 
HETATM 16 C C07 PGW . . . K 6 -44.674 24.954 26.024 1 45.22 ? C07 PGW 502 B 1 
HETATM 17 C C7 PGW . . . K 6 -46.049 19.327 26.164 1 56.57 ? C7 PGW 502 B 1 
HETATM 18 C C08 PGW . . . K 6 -45.428 26.115 25.367 1 47.46 ? C08 PGW 502 B 1 
HETATM 19 C C8 PGW . . . K 6 -46.017 20.853 26.009 1 59.91 ? C8 PGW 502 B 1 
HETATM 20 C C09 PGW . . . K 6 -45.284 27.386 26.209 1 53.31 ? C09 PGW 502 B 1 
HETATM 21 C C9 PGW . . . K 6 -44.603 21.344 26.214 1 52.42 ? C9 PGW 502 B 1 
HETATM 22 C C10 PGW . . . K 6 -44.198 22.519 25.79 1 45.14 ? C10 PGW 502 B 1 
HETATM 23 C C11 PGW . . . K 6 -45.626 28.609 25.353 1 55.91 ? C11 PGW 502 B 1 
HETATM 24 O O11 PGW . . . K 6 -55.922 16.772 27.296 1 78.99 ? O11 PGW 502 B 1 
HETATM 25 C C12 PGW . . . K 6 -45.29 29.898 26.111 1 67.23 ? C12 PGW 502 B 1 
HETATM 26 O O12 PGW . . . K 6 -57.895 15.122 26.652 1 78.88 ? O12 PGW 502 B 1 
HETATM 27 C C13 PGW . . . K 6 -45.226 31.074 25.131 1 52.71 ? C13 PGW 502 B 1 
HETATM 28 O O13 PGW . . . K 6 -58.302 17.592 26.955 1 90.86 ? O13 PGW 502 B 1 
HETATM 29 C C14 PGW . . . K 6 -45.849 32.319 25.767 1 31.98 ? C14 PGW 502 B 1 
HETATM 30 O O14 PGW . . . K 6 -57.809 16.229 28.902 1 102.88 ? O14 PGW 502 B 1 
HETATM 31 C C19 PGW . . . K 6 -51.398 15.312 27.706 1 64.08 ? C19 PGW 502 B 1 
HETATM 32 C C20 PGW . . . K 6 -50.039 15.769 27.25 1 44.54 ? C20 PGW 502 B 1 
HETATM 33 C C21 PGW . . . K 6 -48.983 14.757 27.691 1 50.27 ? C21 PGW 502 B 1 
HETATM 34 C C22 PGW . . . K 6 -47.626 15.462 27.696 1 61.8 ? C22 PGW 502 B 1 
HETATM 35 C C23 PGW . . . K 6 -46.474 14.456 27.617 1 55.5 ? C23 PGW 502 B 1 
HETATM 36 C C24 PGW . . . K 6 -45.162 15.233 27.487 1 45.49 ? C24 PGW 502 B 1 
HETATM 37 C C25 PGW . . . K 6 -43.975 14.276 27.603 1 43.58 ? C25 PGW 502 B 1 
HETATM 38 C C26 PGW . . . K 6 -42.723 15.079 27.966 1 32.85 ? C26 PGW 502 B 1 
HETATM 39 C C27 PGW . . . K 6 -41.485 14.351 27.44 1 41.66 ? C27 PGW 502 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           278 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           39 
#