data_5JDH
#
_model_server_result.job_id            IMl9OSbMjsxKhYedSNI9Dw 
_model_server_result.datetime_utc      '2024-11-26 18:55:57' 
_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          5jdh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"V","auth_seq_id":421}' 
#
_entry.id    5JDH 
#
_exptl.entry_id    5JDH 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              106.12 
_entity.id                          8 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            DI(HYDROXYETHYL)ETHER 
_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         90 
_cell.entry_id            5JDH 
_cell.length_a            49.883 
_cell.length_b            72.218 
_cell.length_c            96.099 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5JDH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      8 
_struct_asym.id                             V 
_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
metalc ? metalc1 A O ALA 47 A ALA 47 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? 
metalc ? metalc2 A OG1 THR 50 A THR 50 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? 
metalc ? metalc3 A O THR 50 A THR 50 1_555 E CA CA . A CA 404 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.323 ? 
metalc ? metalc4 A OG SER 51 A SER 51 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? 
metalc ? metalc5 A OE1 GLU 54 A GLU 54 1_555 E CA CA . A CA 404 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.345 ? 
metalc ? metalc6 A OE2 GLU 54 A GLU 54 1_555 E CA CA . A CA 404 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.396 ? 
metalc ? metalc7 A OE2 GLU 54 A GLU 54 1_555 E CA CA . A CA 404 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.608 ? 
metalc ? metalc8 A O ILE 118 A ILE 118 1_555 D CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
metalc ? metalc9 A OD1 ASP 121 A ASP 121 1_555 D CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? 
metalc ? metalc10 A O GLY 122 A GLY 122 1_555 D CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? 
metalc ? metalc11 A OD2 ASP 127 A ASP 127 1_555 D CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.504 ? 
metalc ? metalc12 A O THR 209 A THR 209 1_555 E CA CA . A CA 404 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.24 ? 
metalc ? metalc13 A OE2 GLU 213 A GLU 213 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? 
metalc ? metalc14 A OE1 GLU 213 A GLU 213 1_555 E CA CA . A CA 404 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc15 A OE2 GLU 213 A GLU 213 1_555 E CA CA . A CA 404 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.542 ? 
metalc ? metalc16 A OE2 GLU 213 A GLU 213 1_555 E CA CA . A CA 404 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.334 ? 
metalc ? metalc17 A OG SER 236 A SER 236 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? 
metalc ? metalc18 A OD1 ASP 240 A ASP 240 1_555 E CA CA . A CA 404 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.819 ? 
metalc ? metalc19 A OD2 ASP 240 A ASP 240 1_555 E CA CA . A CA 404 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.709 ? 
metalc ? metalc20 D CA CA . A CA 403 1_555 X O HOH . A HOH 531 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.764 ? 
metalc ? metalc21 D CA CA . A CA 403 1_555 X O HOH . A HOH 540 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? 
metalc ? metalc22 E CA CA . A CA 404 1_555 X O HOH . A HOH 509 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.516 ? 
#
_chem_comp.formula           'C4 H10 O3' 
_chem_comp.formula_weight    106.12 
_chem_comp.id                PEG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              DI(HYDROXYETHYL)ETHER 
_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 O1 PEG sing 442 n n 
C1 C2 PEG sing 443 n n 
C1 H11 PEG sing 444 n n 
C1 H12 PEG sing 445 n n 
O1 HO1 PEG sing 446 n n 
C2 O2 PEG sing 447 n n 
C2 H21 PEG sing 448 n n 
C2 H22 PEG sing 449 n n 
O2 C3 PEG sing 450 n n 
C3 C4 PEG sing 451 n n 
C3 H31 PEG sing 452 n n 
C3 H32 PEG sing 453 n n 
C4 O4 PEG sing 454 n n 
C4 H41 PEG sing 455 n n 
C4 H42 PEG sing 456 n n 
O4 HO4 PEG sing 457 n n 
#
_atom_sites.entry_id                     5JDH 
_atom_sites.fract_transf_matrix[1][1]    0.020047 
_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]    0.013847 
_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]    0.010406 
_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
B 2 CL A 1 401 1 CL CL . 
C 3 NA A 1 402 2 NA NA . 
D 4 CA A 1 403 1 CA CA . 
E 4 CA A 1 404 2 CA CA . 
F 5 MYS A 1 405 9 MYS FAT . 
G 5 MYS A 1 406 13 MYS FAT . 
H 5 MYS A 1 407 15 MYS FAT . 
I 5 MYS A 1 408 18 MYS FAT . 
J 5 MYS A 1 409 19 MYS FAT . 
K 5 MYS A 1 410 20 MYS FAT . 
L 5 MYS A 1 411 22 MYS FAT . 
M 5 MYS A 1 412 23 MYS FAT . 
N 5 MYS A 1 413 26 MYS FAT . 
O 5 MYS A 1 414 27 MYS FAT . 
P 5 MYS A 1 415 28 MYS FAT . 
Q 5 MYS A 1 416 29 MYS FAT . 
R 6 1PE A 1 417 1 1PE PEG . 
S 6 1PE A 1 418 2 1PE PEG . 
T 7 PE8 A 1 419 3 PE8 PEG . 
U 6 1PE A 1 420 4 1PE PEG . 
V 8 PEG A 1 421 5 PEG PEG . 
W 9 OLC A 1 422 1 OLC MON . 
X 10 HOH A 1 501 57 HOH HOH . 
X 10 HOH A 2 502 14 HOH HOH . 
X 10 HOH A 3 503 4 HOH HOH . 
X 10 HOH A 4 504 17 HOH HOH . 
X 10 HOH A 5 505 18 HOH HOH . 
X 10 HOH A 6 506 8 HOH HOH . 
X 10 HOH A 7 507 49 HOH HOH . 
X 10 HOH A 8 508 2 HOH HOH . 
X 10 HOH A 9 509 54 HOH HOH . 
X 10 HOH A 10 510 27 HOH HOH . 
X 10 HOH A 11 511 21 HOH HOH . 
X 10 HOH A 12 512 20 HOH HOH . 
X 10 HOH A 13 513 41 HOH HOH . 
X 10 HOH A 14 514 1 HOH HOH . 
X 10 HOH A 15 515 6 HOH HOH . 
X 10 HOH A 16 516 11 HOH HOH . 
X 10 HOH A 17 517 22 HOH HOH . 
X 10 HOH A 18 518 23 HOH HOH . 
X 10 HOH A 19 519 28 HOH HOH . 
X 10 HOH A 20 520 47 HOH HOH . 
X 10 HOH A 21 521 10 HOH HOH . 
X 10 HOH A 22 522 33 HOH HOH . 
X 10 HOH A 23 523 5 HOH HOH . 
X 10 HOH A 24 524 13 HOH HOH . 
X 10 HOH A 25 525 24 HOH HOH . 
X 10 HOH A 26 526 15 HOH HOH . 
X 10 HOH A 27 527 32 HOH HOH . 
X 10 HOH A 28 528 34 HOH HOH . 
X 10 HOH A 29 529 29 HOH HOH . 
X 10 HOH A 30 530 26 HOH HOH . 
X 10 HOH A 31 531 7 HOH HOH . 
X 10 HOH A 32 532 16 HOH HOH . 
X 10 HOH A 33 533 55 HOH HOH . 
X 10 HOH A 34 534 30 HOH HOH . 
X 10 HOH A 35 535 45 HOH HOH . 
X 10 HOH A 36 536 12 HOH HOH . 
X 10 HOH A 37 537 53 HOH HOH . 
X 10 HOH A 38 538 37 HOH HOH . 
X 10 HOH A 39 539 35 HOH HOH . 
X 10 HOH A 40 540 3 HOH HOH . 
X 10 HOH A 41 541 46 HOH HOH . 
X 10 HOH A 42 542 25 HOH HOH . 
X 10 HOH A 43 543 56 HOH HOH . 
X 10 HOH A 44 544 40 HOH HOH . 
X 10 HOH A 45 545 36 HOH HOH . 
X 10 HOH A 46 546 50 HOH HOH . 
X 10 HOH A 47 547 19 HOH HOH . 
X 10 HOH A 48 548 31 HOH HOH . 
X 10 HOH A 49 549 43 HOH HOH . 
X 10 HOH A 50 550 9 HOH HOH . 
X 10 HOH A 51 551 38 HOH HOH . 
X 10 HOH A 52 552 51 HOH HOH . 
X 10 HOH A 53 553 52 HOH HOH . 
X 10 HOH A 54 554 44 HOH HOH . 
X 10 HOH A 55 555 42 HOH HOH . 
X 10 HOH A 56 556 48 HOH HOH . 
X 10 HOH A 57 557 39 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 PEG . . . V 8 5.901 5.295 39.96 1 73.02 ? C1 PEG 421 A 1 
HETATM 2 O O1 PEG . . . V 8 5.365 4.613 41.095 1 83.46 ? O1 PEG 421 A 1 
HETATM 3 C C2 PEG . . . V 8 6.64 4.3 39.064 1 63.84 ? C2 PEG 421 A 1 
HETATM 4 O O2 PEG . . . V 8 7.164 4.996 37.931 1 74.69 ? O2 PEG 421 A 1 
HETATM 5 C C3 PEG . . . V 8 7.786 4.073 37.033 1 57.8 ? C3 PEG 421 A 1 
HETATM 6 C C4 PEG . . . V 8 8.215 4.817 35.766 1 65.26 ? C4 PEG 421 A 1 
HETATM 7 O O4 PEG . . . V 8 8.835 3.899 34.862 1 73.3 ? O4 PEG 421 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           342 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           7 
#