data_5JDG
#
_model_server_result.job_id            UyhT5SVj-qA-APbFMmODxg 
_model_server_result.datetime_utc      '2024-11-15 03:37:21' 
_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          5jdg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":401}' 
#
_entry.id    5JDG 
#
_exptl.entry_id    5JDG 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              22.99 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'SODIUM ION' 
_entity.pdbx_number_of_molecules    2 
_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            5JDG 
_cell.length_a            49.477 
_cell.length_b            72.47 
_cell.length_c            96.297 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5JDG 
_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,Y,Z,AA,BA,CA 
_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 B N N 
? 2 C 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 A O ALA 47 A ALA 47 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? 
metalc ? metalc2 A OG1 THR 50 A THR 50 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? 
metalc ? metalc3 A O THR 50 A THR 50 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? 
metalc ? metalc4 A OG SER 51 A SER 51 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? 
metalc ? metalc5 A OE1 GLU 54 A GLU 54 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? 
metalc ? metalc6 A OE2 GLU 54 A GLU 54 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? 
metalc ? metalc7 A O ILE 118 A ILE 118 1_555 BA CA CA . A CA 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? 
metalc ? metalc8 A OD1 ASP 121 A ASP 121 1_555 BA CA CA . A CA 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? 
metalc ? metalc9 A O GLY 122 A GLY 122 1_555 BA CA CA . A CA 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? 
metalc ? metalc10 A OD2 ASP 127 A ASP 127 1_555 BA CA CA . A CA 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? 
metalc ? metalc11 A O THR 209 A THR 209 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? 
metalc ? metalc12 A OE2 GLU 213 A GLU 213 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? 
metalc ? metalc13 A OE1 GLU 213 A GLU 213 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? 
metalc ? metalc14 A OE2 GLU 213 A GLU 213 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? 
metalc ? metalc15 A OG SER 236 A SER 236 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? 
metalc ? metalc16 K O25 OLC . A OLC 410 1_555 BA CA CA . A CA 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? 
metalc ? metalc17 BA CA CA . A CA 427 1_555 CA O HOH . A HOH 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? 
#
_chem_comp.formula           'Na 1' 
_chem_comp.formula_weight    22.99 
_chem_comp.id                NA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'SODIUM ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     5JDG 
_atom_sites.fract_transf_matrix[1][1]    0.020211 
_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]    0.013799 
_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]    0.010385 
_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 NA A 1 401 1 NA NA . 
C 2 NA A 1 402 2 NA NA . 
D 3 1PE A 1 403 1 1PE PEG . 
E 4 PEG A 1 404 2 PEG PEG . 
F 3 1PE A 1 405 3 1PE PEG . 
G 3 1PE A 1 406 4 1PE PEG . 
H 3 1PE A 1 407 5 1PE PEG . 
I 5 OLC A 1 408 1 OLC MON . 
J 5 OLC A 1 409 2 OLC MON . 
K 5 OLC A 1 410 3 OLC MON . 
L 6 MYS A 1 411 15 MYS FAT . 
M 6 MYS A 1 412 25 MYS FAT . 
N 6 MYS A 1 413 26 MYS FAT . 
O 6 MYS A 1 414 28 MYS FAT . 
P 6 MYS A 1 415 31 MYS FAT . 
Q 6 MYS A 1 416 32 MYS FAT . 
R 6 MYS A 1 417 33 MYS FAT . 
S 6 MYS A 1 418 34 MYS FAT . 
T 6 MYS A 1 419 35 MYS FAT . 
U 6 MYS A 1 420 36 MYS FAT . 
V 6 MYS A 1 421 37 MYS FAT . 
W 6 MYS A 1 422 38 MYS FAT . 
X 6 MYS A 1 423 39 MYS FAT . 
Y 6 MYS A 1 424 40 MYS FAT . 
Z 6 MYS A 1 425 41 MYS FAT . 
AA 6 MYS A 1 426 42 MYS FAT . 
BA 7 CA A 1 427 1 CA CA . 
CA 8 HOH A 1 501 29 HOH HOH . 
CA 8 HOH A 2 502 23 HOH HOH . 
CA 8 HOH A 3 503 13 HOH HOH . 
CA 8 HOH A 4 504 12 HOH HOH . 
CA 8 HOH A 5 505 1 HOH HOH . 
CA 8 HOH A 6 506 37 HOH HOH . 
CA 8 HOH A 7 507 40 HOH HOH . 
CA 8 HOH A 8 508 38 HOH HOH . 
CA 8 HOH A 9 509 3 HOH HOH . 
CA 8 HOH A 10 510 4 HOH HOH . 
CA 8 HOH A 11 511 9 HOH HOH . 
CA 8 HOH A 12 512 8 HOH HOH . 
CA 8 HOH A 13 513 5 HOH HOH . 
CA 8 HOH A 14 514 18 HOH HOH . 
CA 8 HOH A 15 515 7 HOH HOH . 
CA 8 HOH A 16 516 15 HOH HOH . 
CA 8 HOH A 17 517 24 HOH HOH . 
CA 8 HOH A 18 518 20 HOH HOH . 
CA 8 HOH A 19 519 14 HOH HOH . 
CA 8 HOH A 20 520 6 HOH HOH . 
CA 8 HOH A 21 521 43 HOH HOH . 
CA 8 HOH A 22 522 10 HOH HOH . 
CA 8 HOH A 23 523 26 HOH HOH . 
CA 8 HOH A 24 524 17 HOH HOH . 
CA 8 HOH A 25 525 2 HOH HOH . 
CA 8 HOH A 26 526 33 HOH HOH . 
CA 8 HOH A 27 527 16 HOH HOH . 
CA 8 HOH A 28 528 11 HOH HOH . 
CA 8 HOH A 29 529 22 HOH HOH . 
CA 8 HOH A 30 530 39 HOH HOH . 
CA 8 HOH A 31 531 35 HOH HOH . 
CA 8 HOH A 32 532 25 HOH HOH . 
CA 8 HOH A 33 533 30 HOH HOH . 
CA 8 HOH A 34 534 28 HOH HOH . 
CA 8 HOH A 35 535 45 HOH HOH . 
CA 8 HOH A 36 536 44 HOH HOH . 
CA 8 HOH A 37 537 32 HOH HOH . 
CA 8 HOH A 38 538 41 HOH HOH . 
CA 8 HOH A 39 539 46 HOH HOH . 
CA 8 HOH A 40 540 36 HOH HOH . 
CA 8 HOH A 41 541 34 HOH HOH . 
CA 8 HOH A 42 542 27 HOH HOH . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           NA 
_atom_site.label_atom_id         NA 
_atom_site.label_comp_id         NA 
_atom_site.label_seq_id          . 
_atom_site.label_alt_id          . 
_atom_site.pdbx_PDB_ins_code     . 
_atom_site.label_asym_id         B 
_atom_site.label_entity_id       2 
_atom_site.Cartn_x               6.723 
_atom_site.Cartn_y               18.319 
_atom_site.Cartn_z               20.018 
_atom_site.occupancy             0.7 
_atom_site.B_iso_or_equiv        41.73 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NA 
_atom_site.auth_comp_id          NA 
_atom_site.auth_seq_id           401 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           1 
#