data_5ON4
#
_model_server_result.job_id            -Ph7tsCtoF646Da9xeK4JQ 
_model_server_result.datetime_utc      '2025-06-24 01:51:36' 
_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          5on4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":602}' 
#
_entry.id    5ON4 
#
_exptl.entry_id    5ON4 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              434.506 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '2-[2-[[2,3-bis(oxidanyl)phenyl]methyl-(2-hydroxy-2-oxoethyl)amino]ethyl-[(2-methylsulfanylphenyl)methyl]amino]ethanoic acid' 
_entity.pdbx_number_of_molecules    2 
_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            5ON4 
_cell.length_a            86.69 
_cell.length_b            94.121 
_cell.length_c            129.545 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5ON4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,K 1 1 
B,G,H,I,J,L 2 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
? 3 D N N 
? 3 H 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
metalc ? metalc1 C FE FE . A FE 601 1_555 D NAL 9YK . A 9YK 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? 
metalc ? metalc2 C FE FE . A FE 601 1_555 D N 9YK . A 9YK 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? 
metalc ? metalc3 C FE FE . A FE 601 1_555 D O 9YK . A 9YK 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? 
metalc ? metalc4 C FE FE . A FE 601 1_555 D OAY 9YK . A 9YK 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
metalc ? metalc5 C FE FE . A FE 601 1_555 E O3 GOL . A GOL 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? 
metalc ? metalc6 G FE FE . B FE 601 1_555 H OAY 9YK . B 9YK 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
metalc ? metalc7 G FE FE . B FE 601 1_555 H N 9YK . B 9YK 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? 
metalc ? metalc8 G FE FE . B FE 601 1_555 H O 9YK . B 9YK 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? 
metalc ? metalc9 G FE FE . B FE 601 1_555 H NAL 9YK . B 9YK 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? 
metalc ? metalc10 G FE FE . B FE 601 1_555 H OBA 9YK . B 9YK 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? 
#
_chem_comp.formula           'C21 H26 N2 O6 S' 
_chem_comp.formula_weight    434.506 
_chem_comp.id                9YK 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '2-[2-[[2,3-bis(oxidanyl)phenyl]methyl-(2-hydroxy-2-oxoethyl)amino]ethyl-[(2-methylsulfanylphenyl)methyl]amino]ethanoic acid' 
_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
OBA CAZ 9YK doub 1 n n 
CAF CAE 9YK doub 2 n y 
CAF CAG 9YK sing 3 n y 
CAH CAG 9YK sing 4 n n 
CAH N 9YK sing 5 n n 
CAE CAQ 9YK sing 6 n y 
CAG CAS 9YK doub 7 n y 
CAJ N 9YK sing 8 n n 
CAJ CAK 9YK sing 9 n n 
CAZ OBD 9YK sing 10 n n 
CAZ CAT 9YK sing 11 n n 
N CA 9YK sing 12 n n 
CAQ CAR 9YK doub 13 n y 
CAS CAR 9YK sing 14 n y 
CAS OAY 9YK sing 15 n n 
CAT NAL 9YK sing 16 n n 
CAK NAL 9YK sing 17 n n 
CA C 9YK sing 18 n n 
CAR OAX 9YK sing 19 n n 
NAL CAM 9YK sing 20 n n 
C O 9YK doub 21 n n 
C OXT 9YK sing 22 n n 
CAO CAP 9YK doub 23 n y 
CAO CAN 9YK sing 24 n y 
CAP CAW 9YK sing 25 n y 
CBE SBB 9YK sing 26 n n 
CAM CAN 9YK sing 27 n n 
CAN CAU 9YK doub 28 n y 
CAW CAV 9YK doub 29 n y 
CAU CAV 9YK sing 30 n y 
CAU SBB 9YK sing 31 n n 
OAX H1 9YK sing 32 n n 
OAY H2 9YK sing 33 n n 
CAQ H3 9YK sing 34 n n 
CAE H4 9YK sing 35 n n 
CAF H5 9YK sing 36 n n 
CAH H6 9YK sing 37 n n 
CAH H7 9YK sing 38 n n 
CA H9 9YK sing 39 n n 
CA H10 9YK sing 40 n n 
OXT H11 9YK sing 41 n n 
CAJ H12 9YK sing 42 n n 
CAJ H13 9YK sing 43 n n 
CAK H14 9YK sing 44 n n 
CAK H15 9YK sing 45 n n 
CAT H17 9YK sing 46 n n 
CAT H18 9YK sing 47 n n 
OBD H19 9YK sing 48 n n 
CAM H20 9YK sing 49 n n 
CAM H21 9YK sing 50 n n 
CAO H22 9YK sing 51 n n 
CAP H23 9YK sing 52 n n 
CAW H24 9YK sing 53 n n 
CAV H25 9YK sing 54 n n 
CBE H26 9YK sing 55 n n 
CBE H27 9YK sing 56 n n 
CBE H28 9YK sing 57 n n 
#
_atom_sites.entry_id                     5ON4 
_atom_sites.fract_transf_matrix[1][1]    0.011535 
_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]    0.010625 
_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]    0.007719 
_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
C 2 FE A 1 601 1 FE FE . 
D 3 9YK A 1 602 1 9YK BHZ . 
E 4 GOL A 1 603 1 GOL GOL . 
F 4 GOL A 1 604 4 GOL GOL . 
G 2 FE B 1 601 2 FE FE . 
H 3 9YK B 1 602 2 9YK BHZ . 
I 4 GOL B 1 603 2 GOL GOL . 
J 4 GOL B 1 604 3 GOL GOL . 
K 5 HOH A 1 701 6 HOH HOH . 
K 5 HOH A 2 702 55 HOH HOH . 
K 5 HOH A 3 703 81 HOH HOH . 
K 5 HOH A 4 704 38 HOH HOH . 
K 5 HOH A 5 705 24 HOH HOH . 
K 5 HOH A 6 706 37 HOH HOH . 
K 5 HOH A 7 707 88 HOH HOH . 
K 5 HOH A 8 708 80 HOH HOH . 
K 5 HOH A 9 709 53 HOH HOH . 
K 5 HOH A 10 710 54 HOH HOH . 
K 5 HOH A 11 711 36 HOH HOH . 
K 5 HOH A 12 712 10 HOH HOH . 
K 5 HOH A 13 713 17 HOH HOH . 
K 5 HOH A 14 714 83 HOH HOH . 
K 5 HOH A 15 715 8 HOH HOH . 
K 5 HOH A 16 716 15 HOH HOH . 
K 5 HOH A 17 717 86 HOH HOH . 
K 5 HOH A 18 718 71 HOH HOH . 
K 5 HOH A 19 719 42 HOH HOH . 
K 5 HOH A 20 720 13 HOH HOH . 
K 5 HOH A 21 721 67 HOH HOH . 
K 5 HOH A 22 722 63 HOH HOH . 
K 5 HOH A 23 723 74 HOH HOH . 
K 5 HOH A 24 724 47 HOH HOH . 
K 5 HOH A 25 725 2 HOH HOH . 
K 5 HOH A 26 726 61 HOH HOH . 
K 5 HOH A 27 727 7 HOH HOH . 
K 5 HOH A 28 728 79 HOH HOH . 
K 5 HOH A 29 729 62 HOH HOH . 
K 5 HOH A 30 730 11 HOH HOH . 
K 5 HOH A 31 731 3 HOH HOH . 
K 5 HOH A 32 732 43 HOH HOH . 
K 5 HOH A 33 733 21 HOH HOH . 
K 5 HOH A 34 734 31 HOH HOH . 
K 5 HOH A 35 735 27 HOH HOH . 
K 5 HOH A 36 736 32 HOH HOH . 
K 5 HOH A 37 737 20 HOH HOH . 
K 5 HOH A 38 738 89 HOH HOH . 
K 5 HOH A 39 739 69 HOH HOH . 
K 5 HOH A 40 740 25 HOH HOH . 
K 5 HOH A 41 741 85 HOH HOH . 
K 5 HOH A 42 742 33 HOH HOH . 
K 5 HOH A 43 743 58 HOH HOH . 
K 5 HOH A 44 744 59 HOH HOH . 
K 5 HOH A 45 745 40 HOH HOH . 
K 5 HOH A 46 746 70 HOH HOH . 
K 5 HOH A 47 747 48 HOH HOH . 
K 5 HOH A 48 748 23 HOH HOH . 
K 5 HOH A 49 749 41 HOH HOH . 
K 5 HOH A 50 750 26 HOH HOH . 
K 5 HOH A 51 751 39 HOH HOH . 
K 5 HOH A 52 752 60 HOH HOH . 
K 5 HOH A 53 753 66 HOH HOH . 
L 5 HOH B 1 701 73 HOH HOH . 
L 5 HOH B 2 702 77 HOH HOH . 
L 5 HOH B 3 703 19 HOH HOH . 
L 5 HOH B 4 704 52 HOH HOH . 
L 5 HOH B 5 705 44 HOH HOH . 
L 5 HOH B 6 706 16 HOH HOH . 
L 5 HOH B 7 707 78 HOH HOH . 
L 5 HOH B 8 708 90 HOH HOH . 
L 5 HOH B 9 709 28 HOH HOH . 
L 5 HOH B 10 710 18 HOH HOH . 
L 5 HOH B 11 711 34 HOH HOH . 
L 5 HOH B 12 712 14 HOH HOH . 
L 5 HOH B 13 713 49 HOH HOH . 
L 5 HOH B 14 714 84 HOH HOH . 
L 5 HOH B 15 715 5 HOH HOH . 
L 5 HOH B 16 716 50 HOH HOH . 
L 5 HOH B 17 717 12 HOH HOH . 
L 5 HOH B 18 718 1 HOH HOH . 
L 5 HOH B 19 719 65 HOH HOH . 
L 5 HOH B 20 720 30 HOH HOH . 
L 5 HOH B 21 721 57 HOH HOH . 
L 5 HOH B 22 722 22 HOH HOH . 
L 5 HOH B 23 723 64 HOH HOH . 
L 5 HOH B 24 724 9 HOH HOH . 
L 5 HOH B 25 725 82 HOH HOH . 
L 5 HOH B 26 726 4 HOH HOH . 
L 5 HOH B 27 727 87 HOH HOH . 
L 5 HOH B 28 728 75 HOH HOH . 
L 5 HOH B 29 729 51 HOH HOH . 
L 5 HOH B 30 730 76 HOH HOH . 
L 5 HOH B 31 731 56 HOH HOH . 
L 5 HOH B 32 732 35 HOH HOH . 
L 5 HOH B 33 733 45 HOH HOH . 
L 5 HOH B 34 734 68 HOH HOH . 
L 5 HOH B 35 735 46 HOH HOH . 
L 5 HOH B 36 736 29 HOH HOH . 
L 5 HOH B 37 737 72 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 CAR 9YK . . . D 3 3.808 1.988 35.59 1 62.91 ? CAR 9YK 602 A 1 
HETATM 2 C CAS 9YK . . . D 3 3.338 0.707 35.292 1 51.41 ? CAS 9YK 602 A 1 
HETATM 3 O OAY 9YK . . . D 3 2.093 0.323 35.731 1 75.56 ? OAY 9YK 602 A 1 
HETATM 4 C CAQ 9YK . . . D 3 5.055 2.394 35.155 1 50.64 ? CAQ 9YK 602 A 1 
HETATM 5 C CAE 9YK . . . D 3 5.854 1.522 34.415 1 52.39 ? CAE 9YK 602 A 1 
HETATM 6 C CAF 9YK . . . D 3 5.391 0.238 34.11 1 61.44 ? CAF 9YK 602 A 1 
HETATM 7 C CAG 9YK . . . D 3 4.134 -0.178 34.543 1 52.87 ? CAG 9YK 602 A 1 
HETATM 8 C CAH 9YK . . . D 3 3.646 -1.574 34.205 1 68.68 ? CAH 9YK 602 A 1 
HETATM 9 N N 9YK . . . D 3 3.339 -2.316 35.429 1 74.37 ? N 9YK 602 A 1 
HETATM 10 C CA 9YK . . . D 3 4.552 -2.567 36.198 1 68.11 ? CA 9YK 602 A 1 
HETATM 11 C C 9YK . . . D 3 4.231 -2.514 37.653 1 56.35 ? C 9YK 602 A 1 
HETATM 12 O OXT 9YK . . . D 3 5.159 -3.06 38.313 1 55.25 ? OXT 9YK 602 A 1 
HETATM 13 O O 9YK . . . D 3 3.129 -1.942 37.823 1 57.11 ? O 9YK 602 A 1 
HETATM 14 C CAJ 9YK . . . D 3 2.671 -3.62 35.148 1 74.19 ? CAJ 9YK 602 A 1 
HETATM 15 C CAK 9YK . . . D 3 1.588 -3.492 34.079 1 81.78 ? CAK 9YK 602 A 1 
HETATM 16 N NAL 9YK . . . D 3 0.516 -2.539 34.478 1 90.79 ? NAL 9YK 602 A 1 
HETATM 17 C CAT 9YK . . . D 3 -0.323 -2.154 33.362 1 87.24 ? CAT 9YK 602 A 1 
HETATM 18 C CAZ 9YK . . . D 3 -0.274 -0.667 33.193 1 78.06 ? CAZ 9YK 602 A 1 
HETATM 19 O OBD 9YK . . . D 3 -0.936 -0.319 32.176 1 69.86 ? OBD 9YK 602 A 1 
HETATM 20 O OBA 9YK . . . D 3 0.414 -0.143 34.106 1 70.32 ? OBA 9YK 602 A 1 
HETATM 21 C CAM 9YK . . . D 3 -0.303 -2.872 35.663 1 100.17 ? CAM 9YK 602 A 1 
HETATM 22 C CAN 9YK . . . D 3 -0.418 -4.339 36.127 1 107.64 ? CAN 9YK 602 A 1 
HETATM 23 C CAO 9YK . . . D 3 -0.827 -5.365 35.273 1 116.29 ? CAO 9YK 602 A 1 
HETATM 24 C CAP 9YK . . . D 3 -0.923 -6.681 35.744 1 109.37 ? CAP 9YK 602 A 1 
HETATM 25 C CAW 9YK . . . D 3 -0.632 -6.973 37.072 1 103.46 ? CAW 9YK 602 A 1 
HETATM 26 C CAV 9YK . . . D 3 -0.238 -5.959 37.939 1 106.91 ? CAV 9YK 602 A 1 
HETATM 27 C CAU 9YK . . . D 3 -0.135 -4.642 37.468 1 111.38 ? CAU 9YK 602 A 1 
HETATM 28 S SBB 9YK . . . D 3 0.362 -3.353 38.571 1 115.71 ? SBB 9YK 602 A 1 
HETATM 29 C CBE 9YK . . . D 3 -1.066 -2.482 39.159 1 111.57 ? CBE 9YK 602 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           324 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           29 
#