data_6S63
#
_model_server_result.job_id            L2TBRhwSLx_14nILi7sbeg 
_model_server_result.datetime_utc      '2025-08-06 03:15:04' 
_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          6s63 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":311}' 
#
_entry.id    6S63 
#
_exptl.entry_id    6S63 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              128.255 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            nonane 
_entity.pdbx_number_of_molecules    5 
_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            6S63 
_cell.length_a            45.91 
_cell.length_b            48.351 
_cell.length_c            105.364 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6S63 
_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 
_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 G N N 
? 4 H N N 
? 4 I N N 
? 4 J N N 
? 4 K 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 A C PCA 1 A PCA 7 1_555 A N ALA 2 A ALA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? 
covale ? covale2 A NZ LYS 220 A LYS 226 1_555 B C15 RET . A RET 300 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.27 ? 
covale ? covale3 A NZ LYS 220 A LYS 226 1_555 B C15 RET . A RET 300 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.27 ? 
metalc ? metalc1 A OD2 ASP 5 A ASP 11 1_555 L CA CA . A CA 713 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? 
metalc ? metalc2 A OD1 ASP 5 A ASP 11 1_555 M NA NA . A NA 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? 
metalc ? metalc3 A OD1 ASP 9 A ASP 15 1_555 M NA NA . A NA 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.636 ? 
metalc ? metalc4 A O ARG 11 A ARG 17 1_555 M NA NA . A NA 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.137 ? 
metalc ? metalc5 A OG1 THR 14 A THR 20 1_555 M NA NA . A NA 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.686 ? 
metalc ? metalc6 A OD1 ASP 40 A ASP 46 1_555 L CA CA . A CA 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.816 ? 
metalc ? metalc7 A OD2 ASP 40 A ASP 46 1_555 L CA CA . A CA 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? 
metalc ? metalc8 A OD2 ASP 42 A ASP 48 1_555 L CA CA . A CA 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? 
metalc ? metalc9 A O LEU 234 A LEU 240 1_555 L CA CA . A CA 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? 
metalc ? metalc10 Q O HOH . A HOH 586 1_555 L CA CA . A CA 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? 
metalc ? metalc11 Q O HOH . A HOH 589 1_555 L CA CA . A CA 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? 
#
_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                     6S63 
_atom_sites.fract_transf_matrix[1][1]    0.021782 
_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]    0.020682 
_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]    0.009491 
_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 R16 A 1 302 302 R16 R16 . 
D 3 R16 A 1 303 303 R16 R16 . 
E 3 R16 A 1 304 304 R16 R16 . 
F 3 R16 A 1 305 305 R16 R16 . 
G 4 DD9 A 1 308 308 DD9 DD9 . 
H 4 DD9 A 1 309 309 DD9 DD9 . 
I 4 DD9 A 1 310 310 DD9 DD9 . 
J 4 DD9 A 1 311 311 DD9 DD9 . 
K 4 DD9 A 1 312 312 DD9 DD9 . 
L 5 CA A 1 713 713 CA CA . 
M 6 NA A 1 714 714 NA NA . 
N 7 CL A 1 715 715 CL CL . 
O 7 CL A 1 716 716 CL CL . 
P 7 CL A 1 717 717 CL CL . 
Q 8 HOH A 1 401 401 HOH HOH . 
Q 8 HOH A 2 402 402 HOH HOH . 
Q 8 HOH A 3 404 404 HOH HOH . 
Q 8 HOH A 4 406 406 HOH HOH . 
Q 8 HOH A 5 407 407 HOH HOH . 
Q 8 HOH A 6 411 411 HOH HOH . 
Q 8 HOH A 7 501 501 HOH HOH . 
Q 8 HOH A 8 512 512 HOH HOH . 
Q 8 HOH A 9 513 513 HOH HOH . 
Q 8 HOH A 10 520 520 HOH HOH . 
Q 8 HOH A 11 523 523 HOH HOH . 
Q 8 HOH A 12 525 525 HOH HOH . 
Q 8 HOH A 13 527 527 HOH HOH . 
Q 8 HOH A 14 528 528 HOH HOH . 
Q 8 HOH A 15 531 531 HOH HOH . 
Q 8 HOH A 16 534 534 HOH HOH . 
Q 8 HOH A 17 536 536 HOH HOH . 
Q 8 HOH A 18 538 538 HOH HOH . 
Q 8 HOH A 19 541 541 HOH HOH . 
Q 8 HOH A 20 544 544 HOH HOH . 
Q 8 HOH A 21 545 545 HOH HOH . 
Q 8 HOH A 22 546 546 HOH HOH . 
Q 8 HOH A 23 547 547 HOH HOH . 
Q 8 HOH A 24 549 549 HOH HOH . 
Q 8 HOH A 25 553 553 HOH HOH . 
Q 8 HOH A 26 554 554 HOH HOH . 
Q 8 HOH A 27 555 555 HOH HOH . 
Q 8 HOH A 28 556 556 HOH HOH . 
Q 8 HOH A 29 558 558 HOH HOH . 
Q 8 HOH A 30 561 561 HOH HOH . 
Q 8 HOH A 31 567 567 HOH HOH . 
Q 8 HOH A 32 575 575 HOH HOH . 
Q 8 HOH A 33 576 576 HOH HOH . 
Q 8 HOH A 34 578 578 HOH HOH . 
Q 8 HOH A 35 580 580 HOH HOH . 
Q 8 HOH A 36 582 582 HOH HOH . 
Q 8 HOH A 37 583 583 HOH HOH . 
Q 8 HOH A 38 584 584 HOH HOH . 
Q 8 HOH A 39 586 586 HOH HOH . 
Q 8 HOH A 40 587 587 HOH HOH . 
Q 8 HOH A 41 588 588 HOH HOH . 
Q 8 HOH A 42 589 589 HOH HOH . 
Q 8 HOH A 43 590 590 HOH HOH . 
Q 8 HOH A 44 591 591 HOH HOH . 
Q 8 HOH A 45 592 592 HOH HOH . 
Q 8 HOH A 46 593 593 HOH HOH . 
Q 8 HOH A 47 594 594 HOH HOH . 
Q 8 HOH A 48 595 595 HOH HOH . 
Q 8 HOH A 49 596 596 HOH HOH . 
Q 8 HOH A 50 598 598 HOH HOH . 
Q 8 HOH A 51 599 599 HOH HOH . 
Q 8 HOH A 52 600 600 HOH HOH . 
Q 8 HOH A 53 601 601 HOH HOH . 
Q 8 HOH A 54 602 602 HOH HOH . 
Q 8 HOH A 55 603 603 HOH HOH . 
Q 8 HOH A 56 604 604 HOH HOH . 
Q 8 HOH A 57 622 622 HOH HOH . 
Q 8 HOH A 58 625 625 HOH HOH . 
Q 8 HOH A 59 626 626 HOH HOH . 
Q 8 HOH A 60 627 627 HOH HOH . 
Q 8 HOH A 61 629 629 HOH HOH . 
Q 8 HOH A 62 630 630 HOH HOH . 
Q 8 HOH A 63 632 632 HOH HOH . 
Q 8 HOH A 64 633 633 HOH HOH . 
Q 8 HOH A 65 634 634 HOH HOH . 
Q 8 HOH A 66 635 635 HOH HOH . 
Q 8 HOH A 67 636 636 HOH HOH . 
Q 8 HOH A 68 637 637 HOH HOH . 
Q 8 HOH A 69 638 638 HOH HOH . 
Q 8 HOH A 70 641 641 HOH HOH . 
Q 8 HOH A 71 642 642 HOH HOH . 
Q 8 HOH A 72 645 645 HOH HOH . 
Q 8 HOH A 73 649 649 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 . . . J 4 17.379 -10.97 -19.551 1 59.32 ? C1 DD9 311 A 1 
HETATM 2 C C2 DD9 . . . J 4 18.377 -10.917 -18.415 1 62.37 ? C2 DD9 311 A 1 
HETATM 3 C C3 DD9 . . . J 4 17.864 -10.225 -17.173 1 59.61 ? C3 DD9 311 A 1 
HETATM 4 C C4 DD9 . . . J 4 18.944 -9.708 -16.25 1 60.02 ? C4 DD9 311 A 1 
HETATM 5 C C5 DD9 . . . J 4 18.473 -9.4 -14.847 1 51.47 ? C5 DD9 311 A 1 
HETATM 6 C C6 DD9 . . . J 4 19.583 -9.049 -13.878 1 50.05 ? C6 DD9 311 A 1 
HETATM 7 C C7 DD9 . . . J 4 19.318 -9.461 -12.448 1 47.41 ? C7 DD9 311 A 1 
HETATM 8 C C8 DD9 . . . J 4 20.479 -9.269 -11.504 1 48.74 ? C8 DD9 311 A 1 
HETATM 9 C C9 DD9 . . . J 4 20.23 -9.798 -10.106 1 49.12 ? C9 DD9 311 A 1 
HETATM 10 H H1 DD9 . . . J 4 17.119 -10.065 -19.798 1 71.32 ? H1 DD9 311 A 1 
HETATM 11 H H1A DD9 . . . J 4 16.591 -11.466 -19.27 1 71.32 ? H1A DD9 311 A 1 
HETATM 12 H H1B DD9 . . . J 4 17.781 -11.411 -20.319 1 71.32 ? H1B DD9 311 A 1 
HETATM 13 H H2 DD9 . . . J 4 19.183 -10.45 -18.725 1 74.98 ? H2 DD9 311 A 1 
HETATM 14 H H2A DD9 . . . J 4 18.636 -11.835 -18.179 1 74.98 ? H2A DD9 311 A 1 
HETATM 15 H H3 DD9 . . . J 4 17.299 -10.853 -16.674 1 71.67 ? H3 DD9 311 A 1 
HETATM 16 H H3A DD9 . . . J 4 17.298 -9.471 -17.446 1 71.67 ? H3A DD9 311 A 1 
HETATM 17 H H4 DD9 . . . J 4 19.326 -8.892 -16.639 1 72.17 ? H4 DD9 311 A 1 
HETATM 18 H H4A DD9 . . . J 4 19.66 -10.377 -16.201 1 72.17 ? H4A DD9 311 A 1 
HETATM 19 H H5 DD9 . . . J 4 17.841 -8.65 -14.886 1 61.91 ? H5 DD9 311 A 1 
HETATM 20 H H5A DD9 . . . J 4 17.987 -10.179 -14.501 1 61.91 ? H5A DD9 311 A 1 
HETATM 21 H H6 DD9 . . . J 4 19.726 -8.079 -13.904 1 60.2 ? H6 DD9 311 A 1 
HETATM 22 H H6A DD9 . . . J 4 20.412 -9.479 -14.18 1 60.2 ? H6A DD9 311 A 1 
HETATM 23 H H7 DD9 . . . J 4 18.554 -8.946 -12.112 1 57.04 ? H7 DD9 311 A 1 
HETATM 24 H H7A DD9 . . . J 4 19.063 -10.408 -12.438 1 57.04 ? H7A DD9 311 A 1 
HETATM 25 H H8 DD9 . . . J 4 20.683 -8.31 -11.448 1 58.63 ? H8 DD9 311 A 1 
HETATM 26 H H8A DD9 . . . J 4 21.267 -9.72 -11.878 1 58.63 ? H8A DD9 311 A 1 
HETATM 27 H H9 DD9 . . . J 4 20.033 -10.75 -10.148 1 59.09 ? H9 DD9 311 A 1 
HETATM 28 H H9A DD9 . . . J 4 19.475 -9.33 -9.709 1 59.09 ? H9A DD9 311 A 1 
HETATM 29 H H9B DD9 . . . J 4 21.022 -9.657 -9.558 1 59.09 ? H9B DD9 311 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           337 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           29 
#