data_7ZY3
#
_model_server_result.job_id            8SMhCbq_WreQEMuDmFCIsQ 
_model_server_result.datetime_utc      '2024-11-17 06:34:47' 
_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          7zy3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":301}' 
#
_entry.id    7ZY3 
#
_exptl.entry_id    7ZY3 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              128.255 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            nonane 
_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            7ZY3 
_cell.length_a            46.2 
_cell.length_b            48.3 
_cell.length_c            104.7 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7ZY3 
_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 
_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                      3 
_struct_asym.id                             C 
_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
covale ? covale1 A C PCA 1 A PCA 7 1_555 A N ALA 2 A ALA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.289 ? 
covale ? covale2 A NZ LYS 220 A LYS 226 1_555 B C15 RET . A RET 300 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.22 ? 
covale ? covale3 A NZ LYS 220 A LYS 226 1_555 B C15 RET . A RET 300 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.226 ? 
metalc ? metalc1 A OD2 ASP 5 A ASP 11 1_555 G CA CA . A CA 713 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? 
metalc ? metalc2 A OD1 ASP 5 A ASP 11 1_555 H NA NA . A NA 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.596 ? 
metalc ? metalc3 A OD1 ASP 9 A ASP 15 1_555 H NA NA . A NA 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? 
metalc ? metalc4 A O ARG 11 A ARG 17 1_555 H NA NA . A NA 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.187 ? 
metalc ? metalc5 A OG1 THR 14 A THR 20 1_555 H NA NA . A NA 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.717 ? 
metalc ? metalc6 A OD1 ASP 40 A ASP 46 1_555 G CA CA . A CA 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.739 ? 
metalc ? metalc7 A OD2 ASP 40 A ASP 46 1_555 G CA CA . A CA 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? 
metalc ? metalc8 A OD2 ASP 42 A ASP 48 1_555 G CA CA . A CA 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? 
metalc ? metalc9 A O LEU 234 A LEU 240 1_555 G CA CA . A CA 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? 
metalc ? metalc10 A OD1 ASP 236 A ASP 242 1_555 I MG MG . A MG 715 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? 
metalc ? metalc11 A O THR 237 A THR 243 1_555 I MG MG . A MG 715 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? 
metalc ? metalc12 M O HOH . A HOH 545 2_554 I MG MG . A MG 715 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.544 ? 
metalc ? metalc13 M O HOH . A HOH 547 1_555 I MG MG . A MG 715 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.72 ? 
metalc ? metalc14 M O HOH . A HOH 586 1_555 G CA CA . A CA 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? 
metalc ? metalc15 M O HOH . A HOH 589 2_554 G CA CA . A CA 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? 
metalc ? metalc16 M O HOH . A HOH 664 1_555 I MG MG . A MG 715 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? 
metalc ? metalc17 M O HOH . A HOH 666 1_555 I MG MG . A MG 715 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.906 ? 
#
_chem_comp.formula           'C9 H20' 
_chem_comp.formula_weight    128.255 
_chem_comp.id                DD9 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              nonane 
_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
C2 C1 DD9 sing 83 n n 
C1 H1 DD9 sing 84 n n 
C1 H1A DD9 sing 85 n n 
C1 H1B DD9 sing 86 n n 
C3 C2 DD9 sing 87 n n 
C2 H2 DD9 sing 88 n n 
C2 H2A DD9 sing 89 n n 
C4 C3 DD9 sing 90 n n 
C3 H3 DD9 sing 91 n n 
C3 H3A DD9 sing 92 n n 
C5 C4 DD9 sing 93 n n 
C4 H4 DD9 sing 94 n n 
C4 H4A DD9 sing 95 n n 
C6 C5 DD9 sing 96 n n 
C5 H5 DD9 sing 97 n n 
C5 H5A DD9 sing 98 n n 
C7 C6 DD9 sing 99 n n 
C6 H6 DD9 sing 100 n n 
C6 H6A DD9 sing 101 n n 
C8 C7 DD9 sing 102 n n 
C7 H7 DD9 sing 103 n n 
C7 H7A DD9 sing 104 n n 
C9 C8 DD9 sing 105 n n 
C8 H8 DD9 sing 106 n n 
C8 H8A DD9 sing 107 n n 
C9 H9 DD9 sing 108 n n 
C9 H9A DD9 sing 109 n n 
C9 H9B DD9 sing 110 n n 
#
_atom_sites.entry_id                     7ZY3 
_atom_sites.fract_transf_matrix[1][1]    0.021645 
_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]    0.020704 
_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]    0.009551 
_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 RET A 1 300 300 RET RET . 
C 3 DD9 A 1 301 301 DD9 DD9 . 
D 4 R16 A 1 302 302 R16 R16 . 
E 5 PLM A 1 303 303 PLM PLM . 
F 5 PLM A 1 304 304 PLM PLM . 
G 6 CA A 1 713 713 CA CA . 
H 7 NA A 1 714 714 NA NA . 
I 8 MG A 1 715 715 MG MG . 
J 9 CL A 1 716 716 CL CL . 
K 9 CL A 1 718 715 CL CL . 
L 9 CL A 1 717 717 CL CL . 
M 10 HOH A 1 661 661 HOH HOH . 
M 10 HOH A 2 644 644 HOH HOH . 
M 10 HOH A 3 402 402 HOH HOH . 
M 10 HOH A 4 665 665 HOH HOH . 
M 10 HOH A 5 664 664 HOH HOH . 
M 10 HOH A 6 561 561 HOH HOH . 
M 10 HOH A 7 558 558 HOH HOH . 
M 10 HOH A 8 595 595 HOH HOH . 
M 10 HOH A 9 592 592 HOH HOH . 
M 10 HOH A 10 547 547 HOH HOH . 
M 10 HOH A 11 601 601 HOH HOH . 
M 10 HOH A 12 528 528 HOH HOH . 
M 10 HOH A 13 512 512 HOH HOH . 
M 10 HOH A 14 525 525 HOH HOH . 
M 10 HOH A 15 406 406 HOH HOH . 
M 10 HOH A 16 575 575 HOH HOH . 
M 10 HOH A 17 630 630 HOH HOH . 
M 10 HOH A 18 545 545 HOH HOH . 
M 10 HOH A 19 594 594 HOH HOH . 
M 10 HOH A 20 622 622 HOH HOH . 
M 10 HOH A 21 587 587 HOH HOH . 
M 10 HOH A 22 603 603 HOH HOH . 
M 10 HOH A 23 407 407 HOH HOH . 
M 10 HOH A 24 539 539 HOH HOH . 
M 10 HOH A 25 646 646 HOH HOH . 
M 10 HOH A 26 604 604 HOH HOH . 
M 10 HOH A 27 596 596 HOH HOH . 
M 10 HOH A 28 401 401 HOH HOH . 
M 10 HOH A 29 588 588 HOH HOH . 
M 10 HOH A 30 501 501 HOH HOH . 
M 10 HOH A 31 543 543 HOH HOH . 
M 10 HOH A 32 593 593 HOH HOH . 
M 10 HOH A 33 591 591 HOH HOH . 
M 10 HOH A 34 635 635 HOH HOH . 
M 10 HOH A 35 645 645 HOH HOH . 
M 10 HOH A 36 600 600 HOH HOH . 
M 10 HOH A 37 628 628 HOH HOH . 
M 10 HOH A 38 602 602 HOH HOH . 
M 10 HOH A 39 531 531 HOH HOH . 
M 10 HOH A 40 625 625 HOH HOH . 
M 10 HOH A 41 589 589 HOH HOH . 
M 10 HOH A 42 666 666 HOH HOH . 
M 10 HOH A 43 590 590 HOH HOH . 
M 10 HOH A 44 598 598 HOH HOH . 
M 10 HOH A 45 641 641 HOH HOH . 
M 10 HOH A 46 586 586 HOH HOH . 
M 10 HOH A 47 649 649 HOH HOH . 
M 10 HOH A 48 627 627 HOH HOH . 
M 10 HOH A 49 520 520 HOH HOH . 
M 10 HOH A 50 599 599 HOH HOH . 
M 10 HOH A 51 513 513 HOH HOH . 
M 10 HOH A 52 636 636 HOH HOH . 
M 10 HOH A 53 534 534 HOH HOH . 
M 10 HOH A 54 522 522 HOH HOH . 
M 10 HOH A 55 404 404 HOH HOH . 
M 10 HOH A 56 633 633 HOH HOH . 
M 10 HOH A 57 583 583 HOH HOH . 
M 10 HOH A 58 576 576 HOH HOH . 
M 10 HOH A 59 660 660 HOH HOH . 
M 10 HOH A 60 541 541 HOH HOH . 
M 10 HOH A 61 639 639 HOH HOH . 
M 10 HOH A 62 566 566 HOH HOH . 
M 10 HOH A 63 629 629 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 DD9 . . . C 3 -21.092 5.257 -11.889 1 71.2 ? C1 DD9 301 A 1 
HETATM 2 C C2 DD9 . . . C 3 -20.031 5.75 -12.878 1 81.04 ? C2 DD9 301 A 1 
HETATM 3 C C3 DD9 . . . C 3 -20.445 5.502 -14.334 1 75.49 ? C3 DD9 301 A 1 
HETATM 4 C C4 DD9 . . . C 3 -19.211 5.683 -15.228 1 60.23 ? C4 DD9 301 A 1 
HETATM 5 C C5 DD9 . . . C 3 -19.473 6.627 -16.394 1 64.53 ? C5 DD9 301 A 1 
HETATM 6 C C6 DD9 . . . C 3 -20.086 5.883 -17.586 1 62.14 ? C6 DD9 301 A 1 
HETATM 7 C C7 DD9 . . . C 3 -19.156 5.881 -18.79 1 56.5 ? C7 DD9 301 A 1 
HETATM 8 C C8 DD9 . . . C 3 -19.969 5.866 -20.096 1 73.1 ? C8 DD9 301 A 1 
HETATM 9 C C9 DD9 . . . C 3 -19.391 4.9 -21.126 1 61.57 ? C9 DD9 301 A 1 
HETATM 10 H H1 DD9 . . . C 3 -21.58 4.516 -12.281 1 85.44 ? H1 DD9 301 A 1 
HETATM 11 H H1A DD9 . . . C 3 -21.707 5.979 -11.688 1 85.44 ? H1A DD9 301 A 1 
HETATM 12 H H1B DD9 . . . C 3 -20.66 4.963 -11.071 1 85.44 ? H1B DD9 301 A 1 
HETATM 13 H H2 DD9 . . . C 3 -19.199 5.282 -12.704 1 97.25 ? H2 DD9 301 A 1 
HETATM 14 H H2A DD9 . . . C 3 -19.899 6.702 -12.747 1 97.25 ? H2A DD9 301 A 1 
HETATM 15 H H3 DD9 . . . C 3 -21.132 6.137 -14.592 1 90.59 ? H3 DD9 301 A 1 
HETATM 16 H H3A DD9 . . . C 3 -20.788 4.6 -14.428 1 90.59 ? H3A DD9 301 A 1 
HETATM 17 H H4 DD9 . . . C 3 -18.951 4.818 -15.58 1 72.29 ? H4 DD9 301 A 1 
HETATM 18 H H4A DD9 . . . C 3 -18.488 6.044 -14.692 1 72.29 ? H4A DD9 301 A 1 
HETATM 19 H H5 DD9 . . . C 3 -18.634 7.028 -16.67 1 77.44 ? H5 DD9 301 A 1 
HETATM 20 H H5A DD9 . . . C 3 -20.085 7.322 -16.106 1 77.44 ? H5A DD9 301 A 1 
HETATM 21 H H6 DD9 . . . C 3 -20.918 6.317 -17.832 1 74.58 ? H6 DD9 301 A 1 
HETATM 22 H H6A DD9 . . . C 3 -20.265 4.966 -17.325 1 74.58 ? H6A DD9 301 A 1 
HETATM 23 H H7 DD9 . . . C 3 -18.592 5.093 -18.757 1 67.8 ? H7 DD9 301 A 1 
HETATM 24 H H7A DD9 . . . C 3 -18.603 6.677 -18.768 1 67.8 ? H7A DD9 301 A 1 
HETATM 25 H H8 DD9 . . . C 3 -19.971 6.76 -20.473 1 87.73 ? H8 DD9 301 A 1 
HETATM 26 H H8A DD9 . . . C 3 -20.879 5.599 -19.894 1 87.73 ? H8A DD9 301 A 1 
HETATM 27 H H9 DD9 . . . C 3 -19.197 4.051 -20.699 1 73.9 ? H9 DD9 301 A 1 
HETATM 28 H H9A DD9 . . . C 3 -18.574 5.271 -21.494 1 73.9 ? H9A DD9 301 A 1 
HETATM 29 H H9B DD9 . . . C 3 -20.034 4.764 -21.839 1 73.9 ? H9B DD9 301 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           277 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           29 
#