data_5NPL
#
_model_server_result.job_id            P5fxm3ciy6h4QRsDd1bEoQ 
_model_server_result.datetime_utc      '2024-11-16 16:16:59' 
_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          5npl 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":303}' 
#
_entry.id    5NPL 
#
_exptl.entry_id    5NPL 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              173.04 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'YTTERBIUM (III) ION' 
_entity.pdbx_number_of_molecules    17 
_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            5NPL 
_cell.length_a            79.89 
_cell.length_b            120.734 
_cell.length_c            117.548 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5NPL 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 3_554 -x,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -58.774 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 D N N 
? 2 F N N 
? 2 H N N 
? 2 I N N 
? 2 J N N 
? 2 K N N 
? 2 L N N 
? 2 M N N 
? 2 N N N 
? 2 O N N 
? 2 P N N 
? 2 Q N N 
? 2 R N N 
? 2 S N N 
? 2 T N N 
? 2 U N N 
? 2 V 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 153 A CYS 153 1_555 A SG CYS 163 A CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? 
disulf ? disulf2 B SG CYS 153 B CYS 153 1_555 B SG CYS 163 B CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf3 C SG CYS 153 C CYS 153 1_555 C SG CYS 163 C CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
metalc ? metalc1 A NH2 ARG 37 A ARG 37 1_555 I YB YB . A YB 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.444 ? 
metalc ? metalc2 A OE2 GLU 42 A GLU 42 1_555 H YB YB . A YB 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.141 ? 
metalc ? metalc3 D YB YB . A YB 301 1_555 E N4 DO3 . A DO3 302 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.413 ? 
metalc ? metalc4 D YB YB . A YB 301 1_555 E O5 DO3 . A DO3 302 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.39 ? 
metalc ? metalc5 D YB YB . A YB 301 1_555 E O7 DO3 . A DO3 302 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.485 ? 
metalc ? metalc6 D YB YB . A YB 301 1_555 E O1 DO3 . A DO3 302 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.116 ? 
metalc ? metalc7 D YB YB . A YB 301 1_555 E N3 DO3 . A DO3 302 1_555 ? ? ? ? A ? ? ? ? ? ? ? 3.388 ? 
metalc ? metalc8 D YB YB . A YB 301 1_555 E N2 DO3 . A DO3 302 1_555 ? ? ? ? A ? ? ? ? ? ? ? 3.413 ? 
metalc ? metalc9 D YB YB . A YB 301 1_555 E O4 DO3 . A DO3 302 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.214 ? 
metalc ? metalc10 F YB YB . A YB 303 1_555 G N2 DO3 . A DO3 304 1_555 ? ? ? ? A ? ? ? ? ? ? ? 3.341 ? 
metalc ? metalc11 F YB YB . A YB 303 1_555 G N3 DO3 . A DO3 304 1_555 ? ? ? ? A ? ? ? ? ? ? ? 3.388 ? 
metalc ? metalc12 F YB YB . A YB 303 1_555 G O5 DO3 . A DO3 304 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.86 ? 
metalc ? metalc13 F YB YB . A YB 303 1_555 G N4 DO3 . A DO3 304 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.359 ? 
metalc ? metalc14 F YB YB . A YB 303 1_555 G N1 DO3 . A DO3 304 1_555 ? ? ? ? A ? ? ? ? ? ? ? 3.422 ? 
metalc ? metalc15 F YB YB . A YB 303 1_555 G O4 DO3 . A DO3 304 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.599 ? 
metalc ? metalc16 F YB YB . A YB 303 1_555 G O1 DO3 . A DO3 304 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.055 ? 
metalc ? metalc17 F YB YB . A YB 303 1_555 G O7 DO3 . A DO3 304 1_555 ? ? ? ? A ? ? ? ? ? ? ? 3.307 ? 
#
_chem_comp.formula           'Yb 3' 
_chem_comp.formula_weight    173.04 
_chem_comp.id                YB 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'YTTERBIUM (III) ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     5NPL 
_atom_sites.fract_transf_matrix[1][1]    0.012517 
_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]    0.008283 
_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]    0.008507 
_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 YB A 1 301 301 YB YB . 
E 3 DO3 A 1 302 302 DO3 DO3 . 
F 2 YB A 1 303 303 YB YB . 
G 3 DO3 A 1 304 304 DO3 DO3 . 
H 2 YB A 1 305 305 YB YB . 
I 2 YB A 1 306 306 YB YB . 
J 2 YB A 1 307 307 YB YB . 
K 2 YB A 1 308 309 YB YB . 
L 2 YB B 1 301 301 YB YB . 
M 2 YB B 1 302 302 YB YB . 
N 2 YB B 1 303 303 YB YB . 
O 2 YB C 1 301 301 YB YB . 
P 2 YB C 1 302 303 YB YB . 
Q 2 YB C 1 303 304 YB YB . 
R 2 YB C 1 304 305 YB YB . 
S 2 YB C 1 305 306 YB YB . 
T 2 YB C 1 306 307 YB YB . 
U 2 YB C 1 307 308 YB YB . 
V 2 YB C 1 308 310 YB YB . 
W 4 HOH A 1 401 1 HOH HOH . 
W 4 HOH A 2 402 2 HOH HOH . 
W 4 HOH A 3 403 18 HOH HOH . 
W 4 HOH A 4 404 5 HOH HOH . 
W 4 HOH A 5 405 7 HOH HOH . 
W 4 HOH A 6 406 3 HOH HOH . 
W 4 HOH A 7 407 4 HOH HOH . 
W 4 HOH A 8 408 9 HOH HOH . 
W 4 HOH A 9 409 6 HOH HOH . 
W 4 HOH A 10 410 10 HOH HOH . 
W 4 HOH A 11 411 8 HOH HOH . 
W 4 HOH A 12 412 11 HOH HOH . 
W 4 HOH A 13 413 12 HOH HOH . 
W 4 HOH A 14 414 13 HOH HOH . 
W 4 HOH A 15 415 27 HOH HOH . 
W 4 HOH A 16 416 14 HOH HOH . 
X 4 HOH B 1 401 16 HOH HOH . 
X 4 HOH B 2 402 17 HOH HOH . 
X 4 HOH B 3 403 15 HOH HOH . 
X 4 HOH B 4 404 19 HOH HOH . 
X 4 HOH B 5 405 20 HOH HOH . 
X 4 HOH B 6 406 21 HOH HOH . 
X 4 HOH B 7 407 22 HOH HOH . 
X 4 HOH B 8 408 24 HOH HOH . 
X 4 HOH B 9 409 23 HOH HOH . 
X 4 HOH B 10 410 25 HOH HOH . 
X 4 HOH B 11 411 26 HOH HOH . 
X 4 HOH B 12 412 28 HOH HOH . 
X 4 HOH B 13 413 29 HOH HOH . 
X 4 HOH B 14 414 30 HOH HOH . 
X 4 HOH B 15 415 31 HOH HOH . 
X 4 HOH B 16 416 32 HOH HOH . 
X 4 HOH B 17 417 33 HOH HOH . 
Y 4 HOH C 1 401 34 HOH HOH . 
Y 4 HOH C 2 402 36 HOH HOH . 
Y 4 HOH C 3 403 37 HOH HOH . 
Y 4 HOH C 4 404 38 HOH HOH . 
Y 4 HOH C 5 405 35 HOH HOH . 
Y 4 HOH C 6 406 40 HOH HOH . 
Y 4 HOH C 7 407 39 HOH HOH . 
Y 4 HOH C 8 408 42 HOH HOH . 
Y 4 HOH C 9 409 43 HOH HOH . 
Y 4 HOH C 10 410 41 HOH HOH . 
Y 4 HOH C 11 411 46 HOH HOH . 
Y 4 HOH C 12 412 47 HOH HOH . 
Y 4 HOH C 13 413 48 HOH HOH . 
Y 4 HOH C 14 414 45 HOH HOH . 
Y 4 HOH C 15 415 44 HOH HOH . 
Y 4 HOH C 16 416 49 HOH HOH . 
Y 4 HOH C 17 417 50 HOH HOH . 
Y 4 HOH C 18 418 51 HOH HOH . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           YB 
_atom_site.label_atom_id         YB 
_atom_site.label_comp_id         YB 
_atom_site.label_seq_id          . 
_atom_site.label_alt_id          C 
_atom_site.pdbx_PDB_ins_code     . 
_atom_site.label_asym_id         Q 
_atom_site.label_entity_id       2 
_atom_site.Cartn_x               34.067 
_atom_site.Cartn_y               -73.689 
_atom_site.Cartn_z               -3.023 
_atom_site.occupancy             0.6 
_atom_site.B_iso_or_equiv        59.79 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          YB 
_atom_site.auth_comp_id          YB 
_atom_site.auth_seq_id           303 
_atom_site.auth_asym_id          C 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              52 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           340 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           1 
#