data_3IK9
#
_model_server_result.job_id            cYoTcgBdtPENaBHTWb-P0A 
_model_server_result.datetime_utc      '2024-11-23 12:08:00' 
_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          3ik9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":503}' 
#
_entry.id    3IK9 
#
_exptl.entry_id    3IK9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              465.562 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(S)-2-amino-5-((R)-1-(carboxymethylamino)-3-((3S,4R)-1,4-dihydroxynonan-3-ylthio)-1-oxopropan-2-ylamino)-5-oxopentanoic acid' 
_entity.pdbx_number_of_molecules    8 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          117.76 
_cell.angle_gamma         90 
_cell.entry_id            3IK9 
_cell.length_a            95.889 
_cell.length_b            114.658 
_cell.length_c            96.239 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3IK9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
PISA dimeric 2 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,I,J,Q,R 1 1 
C,D,K,L,S,T 2 1 
E,F,M,N,U,V 3 1 
G,H,O,P,W,X 4 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
? 2 I N N 
? 2 J N N 
? 2 K N N 
? 2 L N N 
? 2 M N N 
? 2 N N N 
? 2 O N N 
? 2 P N N 
#
_chem_comp.formula           'C19 H35 N3 O8 S' 
_chem_comp.formula_weight    465.562 
_chem_comp.id                BOB 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(S)-2-amino-5-((R)-1-(carboxymethylamino)-3-((3S,4R)-1,4-dihydroxynonan-3-ylthio)-1-oxopropan-2-ylamino)-5-oxopentanoic acid' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     L-gamma-glutamyl-S-[(1S,2R)-2-hydroxy-1-(2-hydroxyethyl)heptyl]-L-cysteinylglycine 
#
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
O11 C1 BOB doub 70 n n 
CA1 C1 BOB sing 71 n n 
C1 O12 BOB sing 72 n n 
N1 CA1 BOB sing 73 n n 
N1 HN1 BOB sing 74 n n 
N1 HN1A BOB sing 75 n n 
CA2 C2 BOB sing 76 n n 
C2 N3 BOB sing 77 n n 
C2 O2 BOB doub 78 n n 
CD1 N2 BOB sing 79 n n 
N2 CA2 BOB sing 80 n n 
N2 HN2 BOB sing 81 n n 
O32 C3 BOB doub 82 n n 
C3 CA3 BOB sing 83 n n 
C3 O31 BOB sing 84 n n 
N3 CA3 BOB sing 85 n n 
N3 HN3 BOB sing 86 n n 
O12 HO12 BOB sing 87 n n 
O31 HO31 BOB sing 88 n n 
C42 C40 BOB sing 89 n n 
C40 SG2 BOB sing 90 n n 
C40 C54 BOB sing 91 n n 
C40 H40 BOB sing 92 n n 
C42 O60 BOB sing 93 n n 
C42 C43 BOB sing 94 n n 
C42 H42 BOB sing 95 n n 
C43 C44 BOB sing 96 n n 
C43 H43 BOB sing 97 n n 
C43 H43A BOB sing 98 n n 
C44 C45 BOB sing 99 n n 
C44 H44 BOB sing 100 n n 
C44 H44A BOB sing 101 n n 
C45 C46 BOB sing 102 n n 
C45 H45 BOB sing 103 n n 
C45 H45A BOB sing 104 n n 
C47 C46 BOB sing 105 n n 
C46 H46 BOB sing 106 n n 
C46 H46A BOB sing 107 n n 
C47 H47 BOB sing 108 n n 
C47 H47A BOB sing 109 n n 
C47 H47B BOB sing 110 n n 
C55 C54 BOB sing 111 n n 
C54 H54 BOB sing 112 n n 
C54 H54A BOB sing 113 n n 
C55 O56 BOB sing 114 n n 
C55 H55 BOB sing 115 n n 
C55 H55A BOB sing 116 n n 
O56 HO56 BOB sing 117 n n 
O60 HO60 BOB sing 118 n n 
CA1 CB1 BOB sing 119 n n 
CA1 HA1 BOB sing 120 n n 
CA2 CB2 BOB sing 121 n n 
CA2 HA2 BOB sing 122 n n 
CA3 HA3 BOB sing 123 n n 
CA3 HA3A BOB sing 124 n n 
CB1 CG1 BOB sing 125 n n 
CB1 HB1 BOB sing 126 n n 
CB1 HB1A BOB sing 127 n n 
SG2 CB2 BOB sing 128 n n 
CB2 HB2 BOB sing 129 n n 
CB2 HB2A BOB sing 130 n n 
OE1 CD1 BOB doub 131 n n 
CG1 CD1 BOB sing 132 n n 
CG1 HG1 BOB sing 133 n n 
CG1 HG1A BOB sing 134 n n 
#
_atom_sites.entry_id                     3IK9 
_atom_sites.fract_transf_matrix[1][1]    0.010429 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00549 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008722 
_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]    0.011742 
_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
I 2 BOB A 1 501 501 BOB BOB . 
J 2 BOB B 1 502 502 BOB BOB . 
K 2 BOB C 1 503 503 BOB BOB . 
L 2 BOB D 1 504 504 BOB BOB . 
M 2 BOB E 1 505 505 BOB BOB . 
N 2 BOB F 1 506 506 BOB BOB . 
O 2 BOB G 1 507 507 BOB BOB . 
P 2 BOB H 1 508 508 BOB BOB . 
Q 3 HOH A 1 6001 6001 HOH HOH . 
Q 3 HOH A 2 6005 6005 HOH HOH . 
Q 3 HOH A 3 6013 6013 HOH HOH . 
Q 3 HOH A 4 6017 6017 HOH HOH . 
Q 3 HOH A 5 6039 6039 HOH HOH . 
Q 3 HOH A 6 6059 6059 HOH HOH . 
R 3 HOH B 1 6003 6003 HOH HOH . 
R 3 HOH B 2 6004 6004 HOH HOH . 
R 3 HOH B 3 6009 6009 HOH HOH . 
R 3 HOH B 4 6010 6010 HOH HOH . 
R 3 HOH B 5 6015 6015 HOH HOH . 
R 3 HOH B 6 6016 6016 HOH HOH . 
R 3 HOH B 7 6021 6021 HOH HOH . 
R 3 HOH B 8 6025 6025 HOH HOH . 
R 3 HOH B 9 6028 6028 HOH HOH . 
R 3 HOH B 10 6040 6040 HOH HOH . 
R 3 HOH B 11 6055 6055 HOH HOH . 
R 3 HOH B 12 6056 6056 HOH HOH . 
R 3 HOH B 13 6057 6057 HOH HOH . 
R 3 HOH B 14 6058 6058 HOH HOH . 
S 3 HOH C 1 6007 6007 HOH HOH . 
S 3 HOH C 2 6008 6008 HOH HOH . 
S 3 HOH C 3 6019 6019 HOH HOH . 
S 3 HOH C 4 6020 6020 HOH HOH . 
S 3 HOH C 5 6027 6027 HOH HOH . 
S 3 HOH C 6 6032 6032 HOH HOH . 
S 3 HOH C 7 6037 6037 HOH HOH . 
S 3 HOH C 8 6038 6038 HOH HOH . 
S 3 HOH C 9 6052 6052 HOH HOH . 
S 3 HOH C 10 6053 6053 HOH HOH . 
S 3 HOH C 11 6054 6054 HOH HOH . 
T 3 HOH D 1 6006 6006 HOH HOH . 
T 3 HOH D 2 6012 6012 HOH HOH . 
T 3 HOH D 3 6014 6014 HOH HOH . 
T 3 HOH D 4 6018 6018 HOH HOH . 
T 3 HOH D 5 6022 6022 HOH HOH . 
T 3 HOH D 6 6033 6033 HOH HOH . 
T 3 HOH D 7 6034 6034 HOH HOH . 
T 3 HOH D 8 6035 6035 HOH HOH . 
T 3 HOH D 9 6036 6036 HOH HOH . 
T 3 HOH D 10 6049 6049 HOH HOH . 
T 3 HOH D 11 6050 6050 HOH HOH . 
T 3 HOH D 12 6051 6051 HOH HOH . 
U 3 HOH E 1 6002 6002 HOH HOH . 
U 3 HOH E 2 6011 6011 HOH HOH . 
U 3 HOH E 3 6023 6023 HOH HOH . 
U 3 HOH E 4 6044 6044 HOH HOH . 
V 3 HOH F 1 6026 6026 HOH HOH . 
V 3 HOH F 2 6029 6029 HOH HOH . 
V 3 HOH F 3 6030 6030 HOH HOH . 
V 3 HOH F 4 6045 6045 HOH HOH . 
V 3 HOH F 5 6046 6046 HOH HOH . 
W 3 HOH G 1 6031 6031 HOH HOH . 
W 3 HOH G 2 6041 6041 HOH HOH . 
W 3 HOH G 3 6042 6042 HOH HOH . 
W 3 HOH G 4 6043 6043 HOH HOH . 
X 3 HOH H 1 6024 6024 HOH HOH . 
X 3 HOH H 2 6047 6047 HOH HOH . 
X 3 HOH H 3 6048 6048 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 BOB . . . K 2 -50.043 -5.547 88.929 1 33.23 ? C1 BOB 503 C 1 
HETATM 2 N N1 BOB . . . K 2 -48.785 -7.592 89.41 1 29.21 ? N1 BOB 503 C 1 
HETATM 3 C C2 BOB . . . K 2 -51.155 -3.831 96.115 1 43.71 ? C2 BOB 503 C 1 
HETATM 4 N N2 BOB . . . K 2 -50.313 -3.778 93.896 1 38.02 ? N2 BOB 503 C 1 
HETATM 5 O O2 BOB . . . K 2 -52.401 -3.648 95.702 1 43.43 ? O2 BOB 503 C 1 
HETATM 6 C C3 BOB . . . K 2 -51.731 -6.44 98.301 1 49.84 ? C3 BOB 503 C 1 
HETATM 7 N N3 BOB . . . K 2 -50.868 -4.407 97.27 1 46.72 ? N3 BOB 503 C 1 
HETATM 8 O O11 BOB . . . K 2 -49.158 -5.18 88.143 1 30.11 ? O11 BOB 503 C 1 
HETATM 9 O O12 BOB . . . K 2 -51.195 -5.078 88.869 1 38.53 ? O12 BOB 503 C 1 
HETATM 10 O O31 BOB . . . K 2 -52.266 -6.992 99.291 1 49.76 ? O31 BOB 503 C 1 
HETATM 11 O O32 BOB . . . K 2 -51.154 -7.093 97.388 1 51.16 ? O32 BOB 503 C 1 
HETATM 12 C C40 BOB . . . K 2 -46.803 -1.426 95.119 1 55.97 ? C40 BOB 503 C 1 
HETATM 13 C C42 BOB . . . K 2 -46.572 -2.596 96.107 1 58.63 ? C42 BOB 503 C 1 
HETATM 14 C C43 BOB . . . K 2 -45.392 -2.445 97.094 1 59.52 ? C43 BOB 503 C 1 
HETATM 15 C C44 BOB . . . K 2 -45.75 -1.795 98.449 1 59.97 ? C44 BOB 503 C 1 
HETATM 16 C C45 BOB . . . K 2 -45.244 -2.563 99.673 1 60.71 ? C45 BOB 503 C 1 
HETATM 17 C C46 BOB . . . K 2 -43.733 -2.394 99.887 1 61.87 ? C46 BOB 503 C 1 
HETATM 18 C C47 BOB . . . K 2 -43.08 -3.636 100.481 1 62.19 ? C47 BOB 503 C 1 
HETATM 19 C C54 BOB . . . K 2 -46.509 -0.013 95.648 1 58 ? C54 BOB 503 C 1 
HETATM 20 C C55 BOB . . . K 2 -45.915 0.897 94.567 1 58.57 ? C55 BOB 503 C 1 
HETATM 21 O O56 BOB . . . K 2 -46.688 2.095 94.461 1 59.83 ? O56 BOB 503 C 1 
HETATM 22 O O60 BOB . . . K 2 -47.751 -2.905 96.863 1 63.35 ? O60 BOB 503 C 1 
HETATM 23 C CA1 BOB . . . K 2 -49.71 -6.604 89.966 1 33.46 ? CA1 BOB 503 C 1 
HETATM 24 C CA2 BOB . . . K 2 -50.018 -3.393 95.265 1 42.96 ? CA2 BOB 503 C 1 
HETATM 25 C CA3 BOB . . . K 2 -51.812 -4.924 98.241 1 47.19 ? CA3 BOB 503 C 1 
HETATM 26 C CB1 BOB . . . K 2 -49.059 -5.975 91.197 1 32.62 ? CB1 BOB 503 C 1 
HETATM 27 C CB2 BOB . . . K 2 -49.874 -1.876 95.314 1 45.25 ? CB2 BOB 503 C 1 
HETATM 28 C CD1 BOB . . . K 2 -49.561 -4.646 93.241 1 31.71 ? CD1 BOB 503 C 1 
HETATM 29 O OE1 BOB . . . K 2 -48.499 -5.19 93.799 1 30.86 ? OE1 BOB 503 C 1 
HETATM 30 C CG1 BOB . . . K 2 -49.995 -4.967 91.845 1 32.41 ? CG1 BOB 503 C 1 
HETATM 31 S SG2 BOB . . . K 2 -48.45 -1.343 94.433 1 48.91 ? SG2 BOB 503 C 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           292 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           31 
#