data_5YTK
#
_model_server_result.job_id            iT7CqMblMFN-SvNeEvJxKw 
_model_server_result.datetime_utc      '2024-11-05 04:18:22' 
_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          5ytk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"W","auth_seq_id":701}' 
#
_entry.id    5YTK 
#
_exptl.entry_id    5YTK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              131.173 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            LEUCINE 
_entity.pdbx_number_of_molecules    6 
_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         120 
_cell.entry_id            5YTK 
_cell.length_a            108.906 
_cell.length_b            108.906 
_cell.length_c            340.564 
_cell.Z_PDB               36 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YTK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    decameric 
_pdbx_struct_assembly.oligomeric_count      10 
_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,DA 
_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
? 4 M N N 
? 4 P N N 
? 4 U N N 
? 4 V N N 
? 4 W N N 
? 4 X 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
covale ? covale1 M C LEU . B LEU 402 1_555 N NZ LYS . B LYS 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? 
covale ? covale2 P C LEU . C LEU 402 1_555 Q NZ LYS . C LYS 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? 
covale ? covale3 G NZ LYS 5 G LYS 642 1_555 U C LEU . G LEU 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? 
covale ? covale4 H NZ LYS 5 J LYS 642 1_555 V C LEU . J LEU 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? 
covale ? covale5 I NZ LYS 5 K LYS 642 1_555 W C LEU . K LEU 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? 
covale ? covale6 J NZ LYS 5 L LYS 642 1_555 X C LEU . L LEU 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? 
metalc ? metalc1 A SG CYS 136 A CYS 256 1_555 K ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.641 ? 
metalc ? metalc2 A SG CYS 139 A CYS 259 1_555 K ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? 
metalc ? metalc3 A SG CYS 160 A CYS 280 1_555 K ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.592 ? 
metalc ? metalc4 A SG CYS 163 A CYS 283 1_555 K ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? 
metalc ? metalc5 B SG CYS 136 B CYS 256 1_555 L ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.657 ? 
metalc ? metalc6 B SG CYS 139 B CYS 259 1_555 L ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? 
metalc ? metalc7 B SG CYS 160 B CYS 280 1_555 L ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? 
metalc ? metalc8 B SG CYS 163 B CYS 283 1_555 L ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? 
metalc ? metalc9 C SG CYS 136 C CYS 256 1_555 O ZN ZN . C ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? 
metalc ? metalc10 C SG CYS 139 C CYS 259 1_555 O ZN ZN . C ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.618 ? 
metalc ? metalc11 C SG CYS 160 C CYS 280 1_555 O ZN ZN . C ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? 
metalc ? metalc12 C SG CYS 163 C CYS 283 1_555 O ZN ZN . C ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.67 ? 
metalc ? metalc13 D SG CYS 136 D CYS 256 1_555 R ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? 
metalc ? metalc14 D SG CYS 139 D CYS 259 1_555 R ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.662 ? 
metalc ? metalc15 D SG CYS 160 D CYS 280 1_555 R ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.634 ? 
metalc ? metalc16 D SG CYS 163 D CYS 283 1_555 R ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? 
metalc ? metalc17 E SG CYS 136 E CYS 256 1_555 S ZN ZN . E ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? 
metalc ? metalc18 E SG CYS 139 E CYS 259 1_555 S ZN ZN . E ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? 
metalc ? metalc19 E SG CYS 160 E CYS 280 1_555 S ZN ZN . E ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.646 ? 
metalc ? metalc20 E SG CYS 163 E CYS 283 1_555 S ZN ZN . E ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.72 ? 
metalc ? metalc21 F SG CYS 136 F CYS 256 1_555 T ZN ZN . F ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.656 ? 
metalc ? metalc22 F SG CYS 139 F CYS 259 1_555 T ZN ZN . F ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.626 ? 
metalc ? metalc23 F SG CYS 160 F CYS 280 1_555 T ZN ZN . F ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? 
metalc ? metalc24 F SG CYS 163 F CYS 283 1_555 T ZN ZN . F ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? 
#
_chem_comp.formula           'C6 H13 N O2' 
_chem_comp.formula_weight    131.173 
_chem_comp.id                LEU 
_chem_comp.mon_nstd_flag     y 
_chem_comp.name              LEUCINE 
_chem_comp.type              'l-peptide linking' 
_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
N CA LEU sing 173 n n 
N H LEU sing 174 n n 
N H2 LEU sing 175 n n 
CA C LEU sing 176 n n 
CA CB LEU sing 177 n n 
CA HA LEU sing 178 n n 
C O LEU doub 179 n n 
C OXT LEU sing 180 n n 
CB CG LEU sing 181 n n 
CB HB2 LEU sing 182 n n 
CB HB3 LEU sing 183 n n 
CG CD1 LEU sing 184 n n 
CG CD2 LEU sing 185 n n 
CG HG LEU sing 186 n n 
CD1 HD11 LEU sing 187 n n 
CD1 HD12 LEU sing 188 n n 
CD1 HD13 LEU sing 189 n n 
CD2 HD21 LEU sing 190 n n 
CD2 HD22 LEU sing 191 n n 
CD2 HD23 LEU sing 192 n n 
OXT HXT LEU sing 193 n n 
#
_atom_sites.entry_id                     5YTK 
_atom_sites.fract_transf_matrix[1][1]    0.009182 
_atom_sites.fract_transf_matrix[1][2]    0.005301 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010603 
_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]    0.002936 
_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
K 3 ZN A 1 401 401 ZN ZN . 
L 3 ZN B 1 401 401 ZN ZN . 
M 4 LEU B 1 402 402 LEU LEU . 
N 5 LYS B 1 403 403 LYS LYS . 
O 3 ZN C 1 401 401 ZN ZN . 
P 4 LEU C 1 402 402 LEU LEU . 
Q 5 LYS C 1 403 403 LYS LYS . 
R 3 ZN D 1 401 401 ZN ZN . 
S 3 ZN E 1 401 401 ZN ZN . 
T 3 ZN F 1 401 401 ZN ZN . 
U 4 LEU G 1 701 402 LEU LEU . 
V 4 LEU J 1 701 402 LEU LEU . 
W 4 LEU K 1 701 402 LEU LEU . 
X 4 LEU L 1 701 402 LEU LEU . 
Y 6 HOH A 1 501 501 HOH HOH . 
Y 6 HOH A 2 502 502 HOH HOH . 
Y 6 HOH A 3 503 503 HOH HOH . 
Y 6 HOH A 4 504 504 HOH HOH . 
Y 6 HOH A 5 505 505 HOH HOH . 
Y 6 HOH A 6 506 506 HOH HOH . 
Y 6 HOH A 7 507 507 HOH HOH . 
Y 6 HOH A 8 508 508 HOH HOH . 
Y 6 HOH A 9 509 509 HOH HOH . 
Y 6 HOH A 10 510 510 HOH HOH . 
Y 6 HOH A 11 511 511 HOH HOH . 
Z 6 HOH B 1 501 501 HOH HOH . 
Z 6 HOH B 2 502 502 HOH HOH . 
Z 6 HOH B 3 503 503 HOH HOH . 
Z 6 HOH B 4 504 504 HOH HOH . 
Z 6 HOH B 5 505 505 HOH HOH . 
Z 6 HOH B 6 506 506 HOH HOH . 
Z 6 HOH B 7 507 507 HOH HOH . 
Z 6 HOH B 8 508 508 HOH HOH . 
Z 6 HOH B 9 509 509 HOH HOH . 
Z 6 HOH B 10 510 510 HOH HOH . 
Z 6 HOH B 11 511 511 HOH HOH . 
Z 6 HOH B 12 512 512 HOH HOH . 
Z 6 HOH B 13 513 513 HOH HOH . 
Z 6 HOH B 14 514 514 HOH HOH . 
Z 6 HOH B 15 515 515 HOH HOH . 
Z 6 HOH B 16 516 516 HOH HOH . 
Z 6 HOH B 17 517 517 HOH HOH . 
Z 6 HOH B 18 518 518 HOH HOH . 
Z 6 HOH B 19 519 519 HOH HOH . 
Z 6 HOH B 20 520 520 HOH HOH . 
Z 6 HOH B 21 521 521 HOH HOH . 
Z 6 HOH B 22 522 522 HOH HOH . 
Z 6 HOH B 23 523 523 HOH HOH . 
Z 6 HOH B 24 524 524 HOH HOH . 
Z 6 HOH B 25 525 525 HOH HOH . 
Z 6 HOH B 26 526 526 HOH HOH . 
AA 6 HOH C 1 501 501 HOH HOH . 
AA 6 HOH C 2 502 502 HOH HOH . 
AA 6 HOH C 3 503 503 HOH HOH . 
AA 6 HOH C 4 504 504 HOH HOH . 
AA 6 HOH C 5 505 505 HOH HOH . 
AA 6 HOH C 6 506 506 HOH HOH . 
AA 6 HOH C 7 507 507 HOH HOH . 
AA 6 HOH C 8 508 508 HOH HOH . 
AA 6 HOH C 9 509 509 HOH HOH . 
AA 6 HOH C 10 510 510 HOH HOH . 
AA 6 HOH C 11 511 511 HOH HOH . 
AA 6 HOH C 12 512 512 HOH HOH . 
AA 6 HOH C 13 513 513 HOH HOH . 
AA 6 HOH C 14 514 514 HOH HOH . 
AA 6 HOH C 15 515 515 HOH HOH . 
AA 6 HOH C 16 516 516 HOH HOH . 
AA 6 HOH C 17 517 517 HOH HOH . 
AA 6 HOH C 18 518 518 HOH HOH . 
AA 6 HOH C 19 519 519 HOH HOH . 
AA 6 HOH C 20 520 520 HOH HOH . 
AA 6 HOH C 21 521 521 HOH HOH . 
AA 6 HOH C 22 522 522 HOH HOH . 
AA 6 HOH C 23 523 523 HOH HOH . 
AA 6 HOH C 24 524 524 HOH HOH . 
AA 6 HOH C 25 525 525 HOH HOH . 
AA 6 HOH C 26 526 526 HOH HOH . 
AA 6 HOH C 27 527 527 HOH HOH . 
AA 6 HOH C 28 528 528 HOH HOH . 
AA 6 HOH C 29 529 529 HOH HOH . 
BA 6 HOH D 1 501 501 HOH HOH . 
BA 6 HOH D 2 502 502 HOH HOH . 
BA 6 HOH D 3 503 503 HOH HOH . 
BA 6 HOH D 4 504 504 HOH HOH . 
BA 6 HOH D 5 505 505 HOH HOH . 
BA 6 HOH D 6 506 506 HOH HOH . 
BA 6 HOH D 7 507 507 HOH HOH . 
BA 6 HOH D 8 508 508 HOH HOH . 
BA 6 HOH D 9 509 509 HOH HOH . 
BA 6 HOH D 10 510 510 HOH HOH . 
BA 6 HOH D 11 511 511 HOH HOH . 
CA 6 HOH E 1 501 501 HOH HOH . 
CA 6 HOH E 2 502 502 HOH HOH . 
CA 6 HOH E 3 503 503 HOH HOH . 
CA 6 HOH E 4 504 504 HOH HOH . 
CA 6 HOH E 5 505 505 HOH HOH . 
CA 6 HOH E 6 506 506 HOH HOH . 
CA 6 HOH E 7 507 507 HOH HOH . 
CA 6 HOH E 8 508 508 HOH HOH . 
CA 6 HOH E 9 509 509 HOH HOH . 
CA 6 HOH E 10 510 510 HOH HOH . 
CA 6 HOH E 11 511 511 HOH HOH . 
DA 6 HOH F 1 501 501 HOH HOH . 
DA 6 HOH F 2 502 502 HOH HOH . 
DA 6 HOH F 3 503 503 HOH HOH . 
DA 6 HOH F 4 504 504 HOH HOH . 
DA 6 HOH F 5 505 505 HOH HOH . 
DA 6 HOH F 6 506 506 HOH HOH . 
DA 6 HOH F 7 507 507 HOH HOH . 
DA 6 HOH F 8 508 508 HOH HOH . 
DA 6 HOH F 9 509 509 HOH HOH . 
DA 6 HOH F 10 510 510 HOH HOH . 
DA 6 HOH F 11 511 511 HOH HOH . 
DA 6 HOH F 12 512 512 HOH HOH . 
DA 6 HOH F 13 513 513 HOH HOH . 
DA 6 HOH F 14 514 514 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 N N LEU . . . W 4 98.318 26.686 42.916 1 86.5 ? N LEU 701 K 1 
HETATM 2 C CA LEU . . . W 4 98.329 25.653 41.959 1 84.28 ? CA LEU 701 K 1 
HETATM 3 C C LEU . . . W 4 97.998 26.266 40.596 1 80.22 ? C LEU 701 K 1 
HETATM 4 O O LEU . . . W 4 97.514 25.588 39.712 1 80.85 ? O LEU 701 K 1 
HETATM 5 C CB LEU . . . W 4 97.31 24.587 42.32 1 80.41 ? CB LEU 701 K 1 
HETATM 6 C CG LEU . . . W 4 97.932 23.387 43.046 1 72.66 ? CG LEU 701 K 1 
HETATM 7 C CD1 LEU . . . W 4 96.954 22.233 43.171 1 69.4 ? CD1 LEU 701 K 1 
HETATM 8 C CD2 LEU . . . W 4 99.197 22.932 42.365 1 68.15 ? CD2 LEU 701 K 1 
#
_model_server_stats.io_time_ms              32 
_model_server_stats.parse_time_ms           31 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           275 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           8 
#