data_7X8I
#
_model_server_result.job_id            46i7QGBEz03AF-4CXfscjA 
_model_server_result.datetime_utc      '2024-10-22 08:51:12' 
_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          7x8i 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":502}' 
#
_entry.id    7X8I 
#
_exptl.entry_id    7X8I 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              288.295 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-[(1R)-4-methyl-1-oxidanyl-pent-3-enyl]-5,8-bis(oxidanyl)naphthalene-1,4-dione 
_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          99.35 
_cell.angle_gamma         90 
_cell.entry_id            7X8I 
_cell.length_a            76.434 
_cell.length_b            84.197 
_cell.length_c            60.524 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7X8I 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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' 2_557 -x,y,-z+2 -1 0 0 0 1 0 0 0 -1 -19.666058 0 119.439794 
#
_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
disulf ? disulf1 A SG CYS 373 A CYS 401 1_555 A SG CYS 388 A CYS 416 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
metalc ? metalc1 A NE2 HIS 198 A HIS 226 1_555 B CO CO . A CO 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.544 ? 
metalc ? metalc2 A NE2 HIS 280 A HIS 308 1_555 B CO CO . A CO 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? 
metalc ? metalc3 A OE1 GLU 366 A GLU 394 1_555 B CO CO . A CO 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? 
metalc ? metalc4 B CO CO . A CO 501 1_555 C O04 FNO . A FNO 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? 
metalc ? metalc5 B CO CO . A CO 501 1_555 C O05 FNO . A FNO 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? 
#
_chem_comp.formula           'C16 H16 O5' 
_chem_comp.formula_weight    288.295 
_chem_comp.id                FNO 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-[(1R)-4-methyl-1-oxidanyl-pent-3-enyl]-5,8-bis(oxidanyl)naphthalene-1,4-dione 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     shikonin 
#
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
C21 C17 FNO sing 83 n n 
C17 C20 FNO sing 84 n n 
C17 C14 FNO doub 85 n n 
C14 C08 FNO sing 86 n n 
C06 O01 FNO sing 87 n n 
C06 C08 FNO sing 88 n n 
C06 C07 FNO sing 89 n n 
C12 C07 FNO doub 90 n n 
C12 C13 FNO sing 91 n n 
C07 C10 FNO sing 92 n n 
O04 C13 FNO doub 93 n n 
C13 C11 FNO sing 94 n n 
C10 O02 FNO doub 95 n n 
C10 C09 FNO sing 96 n n 
C11 C09 FNO doub 97 n y 
C11 C16 FNO sing 98 n y 
C09 C15 FNO sing 99 n y 
O05 C16 FNO sing 100 n n 
C16 C19 FNO doub 101 n y 
C15 O03 FNO sing 102 n n 
C15 C18 FNO doub 103 n y 
C19 C18 FNO sing 104 n y 
C20 H1 FNO sing 105 n n 
C20 H2 FNO sing 106 n n 
C20 H3 FNO sing 107 n n 
C21 H4 FNO sing 108 n n 
C21 H5 FNO sing 109 n n 
C21 H6 FNO sing 110 n n 
C06 H7 FNO sing 111 n n 
C08 H8 FNO sing 112 n n 
C08 H9 FNO sing 113 n n 
C12 H10 FNO sing 114 n n 
C14 H11 FNO sing 115 n n 
C18 H12 FNO sing 116 n n 
C19 H13 FNO sing 117 n n 
O01 H14 FNO sing 118 n n 
O03 H15 FNO sing 119 n n 
O05 H16 FNO sing 120 n n 
#
_atom_sites.entry_id                     7X8I 
_atom_sites.fract_transf_matrix[1][1]    0.013083 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002154 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011877 
_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]    0.016745 
_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 CO A 1 501 501 CO CO . 
C 3 FNO A 1 502 601 FNO LIG . 
D 4 HOH A 1 601 39 HOH HOH . 
D 4 HOH A 2 602 53 HOH HOH . 
D 4 HOH A 3 603 32 HOH HOH . 
D 4 HOH A 4 604 24 HOH HOH . 
D 4 HOH A 5 605 42 HOH HOH . 
D 4 HOH A 6 606 62 HOH HOH . 
D 4 HOH A 7 607 57 HOH HOH . 
D 4 HOH A 8 608 5 HOH HOH . 
D 4 HOH A 9 609 29 HOH HOH . 
D 4 HOH A 10 610 73 HOH HOH . 
D 4 HOH A 11 611 23 HOH HOH . 
D 4 HOH A 12 612 22 HOH HOH . 
D 4 HOH A 13 613 51 HOH HOH . 
D 4 HOH A 14 614 9 HOH HOH . 
D 4 HOH A 15 615 7 HOH HOH . 
D 4 HOH A 16 616 69 HOH HOH . 
D 4 HOH A 17 617 14 HOH HOH . 
D 4 HOH A 18 618 15 HOH HOH . 
D 4 HOH A 19 619 8 HOH HOH . 
D 4 HOH A 20 620 72 HOH HOH . 
D 4 HOH A 21 621 49 HOH HOH . 
D 4 HOH A 22 622 3 HOH HOH . 
D 4 HOH A 23 623 67 HOH HOH . 
D 4 HOH A 24 624 47 HOH HOH . 
D 4 HOH A 25 625 30 HOH HOH . 
D 4 HOH A 26 626 44 HOH HOH . 
D 4 HOH A 27 627 18 HOH HOH . 
D 4 HOH A 28 628 21 HOH HOH . 
D 4 HOH A 29 629 58 HOH HOH . 
D 4 HOH A 30 630 26 HOH HOH . 
D 4 HOH A 31 631 59 HOH HOH . 
D 4 HOH A 32 632 54 HOH HOH . 
D 4 HOH A 33 633 13 HOH HOH . 
D 4 HOH A 34 634 4 HOH HOH . 
D 4 HOH A 35 635 48 HOH HOH . 
D 4 HOH A 36 636 50 HOH HOH . 
D 4 HOH A 37 637 35 HOH HOH . 
D 4 HOH A 38 638 38 HOH HOH . 
D 4 HOH A 39 639 34 HOH HOH . 
D 4 HOH A 40 640 56 HOH HOH . 
D 4 HOH A 41 641 6 HOH HOH . 
D 4 HOH A 42 642 33 HOH HOH . 
D 4 HOH A 43 643 11 HOH HOH . 
D 4 HOH A 44 645 37 HOH HOH . 
D 4 HOH A 45 646 66 HOH HOH . 
D 4 HOH A 46 647 63 HOH HOH . 
D 4 HOH A 47 648 31 HOH HOH . 
D 4 HOH A 48 649 40 HOH HOH . 
D 4 HOH A 49 650 60 HOH HOH . 
D 4 HOH A 50 651 25 HOH HOH . 
D 4 HOH A 51 652 41 HOH HOH . 
D 4 HOH A 52 653 10 HOH HOH . 
D 4 HOH A 53 654 55 HOH HOH . 
D 4 HOH A 54 655 64 HOH HOH . 
D 4 HOH A 55 656 52 HOH HOH . 
D 4 HOH A 56 657 19 HOH HOH . 
D 4 HOH A 57 658 27 HOH HOH . 
D 4 HOH A 58 659 36 HOH HOH . 
D 4 HOH A 59 660 28 HOH HOH . 
D 4 HOH A 60 661 45 HOH HOH . 
D 4 HOH A 61 662 68 HOH HOH . 
D 4 HOH A 62 663 16 HOH HOH . 
D 4 HOH A 63 664 12 HOH HOH . 
D 4 HOH A 64 665 61 HOH HOH . 
D 4 HOH A 65 666 20 HOH HOH . 
D 4 HOH A 66 667 70 HOH HOH . 
D 4 HOH A 67 668 43 HOH HOH . 
D 4 HOH A 68 669 2 HOH HOH . 
D 4 HOH A 69 670 1 HOH HOH . 
D 4 HOH A 70 671 17 HOH HOH . 
D 4 HOH A 71 672 65 HOH HOH . 
D 4 HOH A 72 673 46 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 C10 FNO . . . C 3 3.145 -5.263 83.045 1 81.43 ? C10 FNO 502 A 1 
HETATM 2 C C13 FNO . . . C 3 3.924 -3.84 80.823 1 69.65 ? C13 FNO 502 A 1 
HETATM 3 C C15 FNO . . . C 3 5.467 -5.629 83.626 1 76.6 ? C15 FNO 502 A 1 
HETATM 4 C C17 FNO . . . C 3 -2.46 -3.631 80.96 1 60.18 ? C17 FNO 502 A 1 
HETATM 5 C C20 FNO . . . C 3 -3.553 -4.1 80.013 1 49.21 ? C20 FNO 502 A 1 
HETATM 6 C C21 FNO . . . C 3 -2.676 -2.307 81.696 1 58.85 ? C21 FNO 502 A 1 
HETATM 7 C C06 FNO . . . C 3 0.709 -4.984 82.599 1 68.6 ? C06 FNO 502 A 1 
HETATM 8 C C07 FNO . . . C 3 2.174 -4.731 82.214 1 70.4 ? C07 FNO 502 A 1 
HETATM 9 C C08 FNO . . . C 3 -0.241 -3.891 82.071 1 61.79 ? C08 FNO 502 A 1 
HETATM 10 C C09 FNO . . . C 3 4.498 -5.095 82.783 1 80.92 ? C09 FNO 502 A 1 
HETATM 11 C C11 FNO . . . C 3 4.883 -4.381 81.667 1 76.6 ? C11 FNO 502 A 1 
HETATM 12 C C12 FNO . . . C 3 2.562 -4.018 81.086 1 65.63 ? C12 FNO 502 A 1 
HETATM 13 C C14 FNO . . . C 3 -1.357 -4.363 81.134 1 57.02 ? C14 FNO 502 A 1 
HETATM 14 C C16 FNO . . . C 3 6.231 -4.21 81.392 1 69.37 ? C16 FNO 502 A 1 
HETATM 15 C C18 FNO . . . C 3 6.813 -5.456 83.353 1 73.17 ? C18 FNO 502 A 1 
HETATM 16 C C19 FNO . . . C 3 7.195 -4.745 82.231 1 69.83 ? C19 FNO 502 A 1 
HETATM 17 O O01 FNO . . . C 3 0.37 -6.295 82.203 1 68.8 ? O01 FNO 502 A 1 
HETATM 18 O O02 FNO . . . C 3 2.8 -5.866 83.998 1 87.76 ? O02 FNO 502 A 1 
HETATM 19 O O03 FNO . . . C 3 5.096 -6.353 84.762 1 83.93 ? O03 FNO 502 A 1 
HETATM 20 O O04 FNO . . . C 3 4.295 -3.226 79.876 1 62.96 ? O04 FNO 502 A 1 
HETATM 21 O O05 FNO . . . C 3 6.618 -3.49 80.257 1 66.47 ? O05 FNO 502 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           320 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           21 
#