data_6YU5
#
_model_server_result.job_id            1w6Iop0yAwQle2byNCsilQ 
_model_server_result.datetime_utc      '2024-10-14 09:21:15' 
_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          6yu5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"V","auth_seq_id":502}' 
#
_entry.id    6YU5 
#
_exptl.entry_id    6YU5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              22.99 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'SODIUM ION' 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90.02 
_cell.angle_gamma         90 
_cell.entry_id            6YU5 
_cell.length_a            44.16 
_cell.length_b            216.03 
_cell.length_c            50.36 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YU5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
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 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,EA 1 1 
B,U,V,W,X,Y,Z,AA,BA,CA,DA,FA 2 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 D N N 
? 3 E N N 
? 3 V N N 
? 3 W 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 GLY 26 A GLY 24 1_555 D NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
metalc ? metalc2 A O ALA 28 A ALA 26 1_555 E NA NA . A NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? 
metalc ? metalc3 A O VAL 29 A VAL 27 1_555 D NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? 
metalc ? metalc4 A OD1 ASN 33 A ASN 31 1_555 E NA NA . A NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? 
metalc ? metalc5 A O THR 233 A THR 231 1_555 E NA NA . A NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? 
metalc ? metalc6 A OG1 THR 233 A THR 231 1_555 E NA NA . A NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? 
metalc ? metalc7 A OD1 ASP 265 A ASP 263 1_555 E NA NA . A NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? 
metalc ? metalc8 A O ALA 322 A ALA 320 1_555 D NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? 
metalc ? metalc9 A OG SER 325 A SER 323 1_555 D NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? 
metalc ? metalc10 A OG SER 326 A SER 324 1_555 D NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? 
metalc ? metalc11 C O VAL . A VAL 501 1_555 E NA NA . A NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? 
metalc ? metalc12 B O GLY 26 B GLY 24 1_555 W NA NA . B NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? 
metalc ? metalc13 B O ALA 28 B ALA 26 1_555 V NA NA . B NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.586 ? 
metalc ? metalc14 B O VAL 29 B VAL 27 1_555 W NA NA . B NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? 
metalc ? metalc15 B OD1 ASN 33 B ASN 31 1_555 V NA NA . B NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? 
metalc ? metalc16 B O THR 233 B THR 231 1_555 V NA NA . B NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? 
metalc ? metalc17 B OG1 THR 233 B THR 231 1_555 V NA NA . B NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? 
metalc ? metalc18 B OD1 ASP 265 B ASP 263 1_555 V NA NA . B NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? 
metalc ? metalc19 B O ALA 322 B ALA 320 1_555 W NA NA . B NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? 
metalc ? metalc20 B OG SER 325 B SER 323 1_555 W NA NA . B NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? 
metalc ? metalc21 B OG SER 326 B SER 324 1_555 W NA NA . B NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? 
metalc ? metalc22 U O VAL . B VAL 501 1_555 V NA NA . B NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? 
#
_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                     6YU5 
_atom_sites.fract_transf_matrix[1][1]    0.022645 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000008 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.004629 
_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]    0.019857 
_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
C 2 VAL A 1 501 2 VAL VAL . 
D 3 NA A 1 502 2 NA NA . 
E 3 NA A 1 503 4 NA NA . 
F 4 BNG A 1 504 2 BNG BNG . 
G 4 BNG A 1 505 4 BNG BNG . 
H 4 BNG A 1 506 5 BNG BNG . 
I 4 BNG A 1 507 8 BNG BNG . 
J 4 BNG A 1 508 9 BNG BNG . 
K 4 BNG A 1 509 10 BNG BNG . 
L 4 BNG A 1 510 14 BNG BNG . 
M 4 BNG A 1 511 20 BNG BNG . 
N 4 BNG A 1 512 21 BNG BNG . 
O 4 BNG A 1 513 22 BNG BNG . 
P 4 BNG A 1 514 26 BNG BNG . 
Q 4 BNG A 1 515 27 BNG BNG . 
R 4 BNG A 1 516 30 BNG BNG . 
S 5 LMT A 1 517 4 LMT LMT . 
T 5 LMT A 1 518 5 LMT LMT . 
U 2 VAL B 1 501 1 VAL VAL . 
V 3 NA B 1 502 1 NA NA . 
W 3 NA B 1 503 3 NA NA . 
X 4 BNG B 1 504 1 BNG BNG . 
Y 4 BNG B 1 505 13 BNG BNG . 
Z 4 BNG B 1 506 16 BNG BNG . 
AA 4 BNG B 1 507 19 BNG BNG . 
BA 4 BNG B 1 508 24 BNG BNG . 
CA 4 BNG B 1 509 28 BNG BNG . 
DA 4 BNG B 1 510 29 BNG BNG . 
EA 6 HOH A 1 601 48 HOH HOH . 
EA 6 HOH A 2 602 58 HOH HOH . 
EA 6 HOH A 3 603 24 HOH HOH . 
EA 6 HOH A 4 604 25 HOH HOH . 
EA 6 HOH A 5 605 112 HOH HOH . 
EA 6 HOH A 6 606 41 HOH HOH . 
EA 6 HOH A 7 607 2 HOH HOH . 
EA 6 HOH A 8 608 32 HOH HOH . 
EA 6 HOH A 9 609 86 HOH HOH . 
EA 6 HOH A 10 610 33 HOH HOH . 
EA 6 HOH A 11 611 45 HOH HOH . 
EA 6 HOH A 12 612 26 HOH HOH . 
EA 6 HOH A 13 613 46 HOH HOH . 
EA 6 HOH A 14 614 36 HOH HOH . 
EA 6 HOH A 15 615 1 HOH HOH . 
EA 6 HOH A 16 616 101 HOH HOH . 
EA 6 HOH A 17 617 34 HOH HOH . 
EA 6 HOH A 18 618 28 HOH HOH . 
EA 6 HOH A 19 619 61 HOH HOH . 
EA 6 HOH A 20 620 136 HOH HOH . 
EA 6 HOH A 21 621 30 HOH HOH . 
EA 6 HOH A 22 622 22 HOH HOH . 
EA 6 HOH A 23 623 35 HOH HOH . 
EA 6 HOH A 24 624 85 HOH HOH . 
EA 6 HOH A 25 625 128 HOH HOH . 
EA 6 HOH A 26 626 27 HOH HOH . 
EA 6 HOH A 27 627 82 HOH HOH . 
EA 6 HOH A 28 628 14 HOH HOH . 
EA 6 HOH A 29 629 76 HOH HOH . 
EA 6 HOH A 30 630 132 HOH HOH . 
EA 6 HOH A 31 631 100 HOH HOH . 
EA 6 HOH A 32 632 53 HOH HOH . 
EA 6 HOH A 33 633 115 HOH HOH . 
EA 6 HOH A 34 634 44 HOH HOH . 
EA 6 HOH A 35 635 102 HOH HOH . 
EA 6 HOH A 36 636 43 HOH HOH . 
EA 6 HOH A 37 637 79 HOH HOH . 
EA 6 HOH A 38 638 107 HOH HOH . 
FA 6 HOH B 1 601 131 HOH HOH . 
FA 6 HOH B 2 602 49 HOH HOH . 
FA 6 HOH B 3 603 40 HOH HOH . 
FA 6 HOH B 4 604 21 HOH HOH . 
FA 6 HOH B 5 605 52 HOH HOH . 
FA 6 HOH B 6 606 10 HOH HOH . 
FA 6 HOH B 7 607 69 HOH HOH . 
FA 6 HOH B 8 608 38 HOH HOH . 
FA 6 HOH B 9 609 12 HOH HOH . 
FA 6 HOH B 10 610 13 HOH HOH . 
FA 6 HOH B 11 611 18 HOH HOH . 
FA 6 HOH B 12 612 66 HOH HOH . 
FA 6 HOH B 13 613 94 HOH HOH . 
FA 6 HOH B 14 614 116 HOH HOH . 
FA 6 HOH B 15 615 39 HOH HOH . 
FA 6 HOH B 16 616 5 HOH HOH . 
FA 6 HOH B 17 617 93 HOH HOH . 
FA 6 HOH B 18 618 23 HOH HOH . 
FA 6 HOH B 19 619 92 HOH HOH . 
FA 6 HOH B 20 620 7 HOH HOH . 
FA 6 HOH B 21 621 54 HOH HOH . 
FA 6 HOH B 22 622 6 HOH HOH . 
FA 6 HOH B 23 623 65 HOH HOH . 
FA 6 HOH B 24 624 122 HOH HOH . 
FA 6 HOH B 25 625 104 HOH HOH . 
FA 6 HOH B 26 626 106 HOH HOH . 
FA 6 HOH B 27 627 73 HOH HOH . 
FA 6 HOH B 28 628 135 HOH HOH . 
FA 6 HOH B 29 629 4 HOH HOH . 
FA 6 HOH B 30 630 74 HOH HOH . 
FA 6 HOH B 31 631 17 HOH HOH . 
FA 6 HOH B 32 632 125 HOH HOH . 
FA 6 HOH B 33 633 134 HOH HOH . 
FA 6 HOH B 34 634 16 HOH HOH . 
FA 6 HOH B 35 635 51 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         V 
_atom_site.label_entity_id       3 
_atom_site.Cartn_x               21.379 
_atom_site.Cartn_y               -81.352 
_atom_site.Cartn_z               1.24 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        52.66 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NA 
_atom_site.auth_comp_id          NA 
_atom_site.auth_seq_id           502 
_atom_site.auth_asym_id          B 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           266 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           1 
#