data_6G8N
#
_model_server_result.job_id            z4YJrsvzZ0BlKX0D5Slfiw 
_model_server_result.datetime_utc      '2024-11-04 23:46:30' 
_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          6g8n 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"EA","auth_seq_id":301}' 
#
_entry.id    6G8N 
#
_exptl.entry_id    6G8N 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              478.578 
_entity.id                          17 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2~{S},3~{S})-3-methyl-2-[(1~{R})-2-[[(2~{S})-3-methyl-1-[[(2~{S})-3-methyl-1-oxidanylidene-1-phenylmethoxy-butan-2-yl] amino]-1-oxidanylidene-butan-2-yl]amino]-1-oxidanyl-2-oxidanylidene-ethyl]pentanoic acid' 
_entity.pdbx_number_of_molecules    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          112.82 
_cell.angle_gamma         90 
_cell.entry_id            6G8N 
_cell.length_a            136.22 
_cell.length_b            302.72 
_cell.length_c            143.97 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6G8N 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    28-meric 
_pdbx_struct_assembly.oligomeric_count      28 
_pdbx_struct_assembly.details               author_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,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA 
_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
? 17 EA N N 
? 17 GA N N 
? 17 IA N N 
? 17 LA N N 
? 17 OA N N 
? 17 RA 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 H OG1 THR 1 H THR 1 1_555 EA C1 EQB . H EQB 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? 
covale ? covale2 K OG1 THR 1 K THR 1 1_555 GA C1 EQB . K EQB 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? 
covale ? covale3 N OG1 THR 1 N THR 1 1_555 IA C1 EQB . N EQB 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? 
covale ? covale4 V OG1 THR 1 V THR 1 1_555 LA C1 EQB . V EQB 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.356 ? 
covale ? covale5 Y OG1 THR 1 Y THR 1 1_555 OA C1 EQB . Y EQB 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
covale ? covale6 BA OG1 THR 1 b THR 1 1_555 RA C1 EQB . b EQB 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? 
metalc ? metalc1 G OG1 THR 17 G THR 8 1_555 CA MG MG . G MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? 
metalc ? metalc2 G O TYR 128 G TYR 119 1_555 CA MG MG . G MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.783 ? 
metalc ? metalc3 G O ARG 131 G ARG 122 1_555 CA MG MG . G MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.781 ? 
metalc ? metalc4 G O MET 134 G MET 125 1_555 CA MG MG . G MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? 
metalc ? metalc5 I O ASP 205 I ASP 204 1_555 PA MG MG . Y MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? 
metalc ? metalc6 K O ALA 165 K ALA 165 1_555 HA MG MG . K MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? 
metalc ? metalc7 K O HIS 166 K HIS 166 1_555 HA MG MG . K MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.921 ? 
metalc ? metalc8 K O ASP 168 K ASP 168 1_555 HA MG MG . K MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.607 ? 
metalc ? metalc9 HA MG MG . K MG 302 1_555 W O ASP 205 W ASP 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.666 ? 
metalc ? metalc10 L OXT ASP 222 L ASP 222 1_555 MA MG MG . V MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
metalc ? metalc11 N O ILE 163 N ILE 163 1_555 JA MG MG . N MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.891 ? 
metalc ? metalc12 N O ASP 166 N ASP 166 1_555 JA MG MG . N MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.907 ? 
metalc ? metalc13 N O SER 169 N SER 169 1_555 JA MG MG . N MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? 
metalc ? metalc14 V O ILE 163 V ILE 163 1_555 MA MG MG . V MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc15 V O ASP 166 V ASP 166 1_555 MA MG MG . V MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? 
metalc ? metalc16 W O ALA 175 W ALA 174 1_555 NA MG MG . W MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.933 ? 
metalc ? metalc17 W O ASP 178 W ASP 177 1_555 NA MG MG . W MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.861 ? 
metalc ? metalc18 Y O ALA 165 Y ALA 165 1_555 PA MG MG . Y MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? 
metalc ? metalc19 Y O ASP 168 Y ASP 168 1_555 PA MG MG . Y MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? 
metalc ? metalc20 Z O THR 192 Z THR 192 1_555 QA MG MG . Z MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.848 ? 
metalc ? metalc21 Z O HIS 195 Z HIS 195 1_555 QA MG MG . Z MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? 
metalc ? metalc22 Z O VAL 198 Z VAL 198 1_555 QA MG MG . Z MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? 
#
_chem_comp.formula           'C25 H38 N2 O7' 
_chem_comp.formula_weight    478.578 
_chem_comp.id                EQB 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2~{S},3~{S})-3-methyl-2-[(1~{R})-2-[[(2~{S})-3-methyl-1-[[(2~{S})-3-methyl-1-oxidanylidene-1-phenylmethoxy-butan-2-yl] amino]-1-oxidanylidene-butan-2-yl]amino]-1-oxidanyl-2-oxidanylidene-ethyl]pentanoic acid' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'Cystargolide B Derivative' 
#
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
O12 C11 EQB doub 83 n n 
C6 C5 EQB sing 84 n n 
C17 C15 EQB sing 85 n n 
C9 C11 EQB sing 86 n n 
C9 O10 EQB sing 87 n n 
C9 C4 EQB sing 88 n n 
C11 N13 EQB sing 89 n n 
C5 C4 EQB sing 90 n n 
C5 C7 EQB sing 91 n n 
C4 C1 EQB sing 92 n n 
C15 C14 EQB sing 93 n n 
C15 C16 EQB sing 94 n n 
N13 C14 EQB sing 95 n n 
C14 C18 EQB sing 96 n n 
C7 C8 EQB sing 97 n n 
C1 O3 EQB doub 98 n n 
C18 N20 EQB sing 99 n n 
C18 O19 EQB doub 100 n n 
N20 C21 EQB sing 101 n n 
C24 C22 EQB sing 102 n n 
O26 C25 EQB doub 103 n n 
C21 C22 EQB sing 104 n n 
C21 C25 EQB sing 105 n n 
C22 C23 EQB sing 106 n n 
C25 O27 EQB sing 107 n n 
O27 C28 EQB sing 108 n n 
C28 C29 EQB sing 109 n n 
C29 C30 EQB doub 110 n y 
C29 C34 EQB sing 111 n y 
C30 C31 EQB sing 112 n y 
C34 C33 EQB doub 113 n y 
C31 C32 EQB doub 114 n y 
C33 C32 EQB sing 115 n y 
C4 H1 EQB sing 116 n n 
C5 H2 EQB sing 117 n n 
C6 H3 EQB sing 118 n n 
C6 H4 EQB sing 119 n n 
C6 H5 EQB sing 120 n n 
C7 H6 EQB sing 121 n n 
C7 H7 EQB sing 122 n n 
C8 H8 EQB sing 123 n n 
C8 H9 EQB sing 124 n n 
C8 H10 EQB sing 125 n n 
C15 H11 EQB sing 126 n n 
C17 H12 EQB sing 127 n n 
C17 H13 EQB sing 128 n n 
C17 H14 EQB sing 129 n n 
C21 H15 EQB sing 130 n n 
C22 H16 EQB sing 131 n n 
C24 H17 EQB sing 132 n n 
C24 H18 EQB sing 133 n n 
C24 H19 EQB sing 134 n n 
C28 H20 EQB sing 135 n n 
C28 H21 EQB sing 136 n n 
C9 H23 EQB sing 137 n n 
O10 H24 EQB sing 138 n n 
N13 H25 EQB sing 139 n n 
C14 H26 EQB sing 140 n n 
C16 H27 EQB sing 141 n n 
C16 H28 EQB sing 142 n n 
C16 H29 EQB sing 143 n n 
N20 H30 EQB sing 144 n n 
C23 H31 EQB sing 145 n n 
C23 H32 EQB sing 146 n n 
C23 H33 EQB sing 147 n n 
C30 H34 EQB sing 148 n n 
C31 H35 EQB sing 149 n n 
C32 H36 EQB sing 150 n n 
C33 H37 EQB sing 151 n n 
C34 H38 EQB sing 152 n n 
C1 OXT EQB sing 153 n n 
OXT HXT EQB sing 154 n n 
#
_atom_sites.entry_id                     6G8N 
_atom_sites.fract_transf_matrix[1][1]    0.007341 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003088 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.003303 
_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]    0.007535 
_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
CA 15 MG G 1 301 6 MG MG . 
DA 16 CL G 1 302 9 CL CL . 
EA 17 EQB H 1 301 1 EQB LIG . 
FA 15 MG I 1 301 7 MG MG . 
GA 17 EQB K 1 301 1 EQB LIG . 
HA 15 MG K 1 302 1 MG MG . 
IA 17 EQB N 1 201 1 EQB LIG . 
JA 15 MG N 1 202 5 MG MG . 
KA 16 CL U 1 301 10 CL CL . 
LA 17 EQB V 1 301 1 EQB LIG . 
MA 15 MG V 1 302 2 MG MG . 
NA 15 MG W 1 301 8 MG MG . 
OA 17 EQB Y 1 301 1 EQB LIG . 
PA 15 MG Y 1 302 4 MG MG . 
QA 15 MG Z 1 301 3 MG MG . 
RA 17 EQB b 1 201 1 EQB LIG . 
#
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 C4 EQB . . . EA 17 63.208 -136.488 41.904 1 74.23 ? C4 EQB 301 H 1 
HETATM 2 C C5 EQB . . . EA 17 64.074 -135.279 41.89 1 72.4 ? C5 EQB 301 H 1 
HETATM 3 C C6 EQB . . . EA 17 64.104 -134.696 40.506 1 69.96 ? C6 EQB 301 H 1 
HETATM 4 C C7 EQB . . . EA 17 63.305 -134.369 42.807 1 75.8 ? C7 EQB 301 H 1 
HETATM 5 C C8 EQB . . . EA 17 63.995 -133.035 42.959 1 79.56 ? C8 EQB 301 H 1 
HETATM 6 C C15 EQB . . . EA 17 61.969 -141.749 41.996 1 70.94 ? C15 EQB 301 H 1 
HETATM 7 C C17 EQB . . . EA 17 62.44 -141.856 40.565 1 72.69 ? C17 EQB 301 H 1 
HETATM 8 C C21 EQB . . . EA 17 59.022 -140.176 45.054 1 76.09 ? C21 EQB 301 H 1 
HETATM 9 C C22 EQB . . . EA 17 57.995 -139.112 45.153 1 76.31 ? C22 EQB 301 H 1 
HETATM 10 C C24 EQB . . . EA 17 56.97 -139.451 44.103 1 73.84 ? C24 EQB 301 H 1 
HETATM 11 C C28 EQB . . . EA 17 57.579 -143.099 46.766 1 96.36 ? C28 EQB 301 H 1 
HETATM 12 C C1 EQB . . . EA 17 63.188 -136.971 43.309 1 77.94 ? C1 EQB 301 H 1 
HETATM 13 O O3 EQB . . . EA 17 62.373 -136.548 44.11 1 80.75 ? O3 EQB 301 H 1 
HETATM 14 C C9 EQB . . . EA 17 63.624 -137.599 40.985 1 73.69 ? C9 EQB 301 H 1 
HETATM 15 O O10 EQB . . . EA 17 64.731 -138.218 41.571 1 68.56 ? O10 EQB 301 H 1 
HETATM 16 C C11 EQB . . . EA 17 62.509 -138.602 41.013 1 71.11 ? C11 EQB 301 H 1 
HETATM 17 O O12 EQB . . . EA 17 61.713 -138.624 40.094 1 75.84 ? O12 EQB 301 H 1 
HETATM 18 N N13 EQB . . . EA 17 62.424 -139.389 42.072 1 69.32 ? N13 EQB 301 H 1 
HETATM 19 C C14 EQB . . . EA 17 61.382 -140.402 42.213 1 69.22 ? C14 EQB 301 H 1 
HETATM 20 C C16 EQB . . . EA 17 60.88 -142.738 42.276 1 71.32 ? C16 EQB 301 H 1 
HETATM 21 C C18 EQB . . . EA 17 60.842 -140.45 43.59 1 67.52 ? C18 EQB 301 H 1 
HETATM 22 O O19 EQB . . . EA 17 61.516 -140.859 44.509 1 59.43 ? O19 EQB 301 H 1 
HETATM 23 N N20 EQB . . . EA 17 59.584 -140.141 43.725 1 69.61 ? N20 EQB 301 H 1 
HETATM 24 C C23 EQB . . . EA 17 57.385 -139.236 46.525 1 78.87 ? C23 EQB 301 H 1 
HETATM 25 C C25 EQB . . . EA 17 58.297 -141.457 45.245 1 85.66 ? C25 EQB 301 H 1 
HETATM 26 O O26 EQB . . . EA 17 57.82 -142.031 44.29 1 98.67 ? O26 EQB 301 H 1 
HETATM 27 O O27 EQB . . . EA 17 58.202 -141.849 46.525 1 101.62 ? O27 EQB 301 H 1 
HETATM 28 C C29 EQB . . . EA 17 57.386 -143.252 48.136 1 93.62 ? C29 EQB 301 H 1 
HETATM 29 C C30 EQB . . . EA 17 57.285 -144.502 48.69 1 85.29 ? C30 EQB 301 H 1 
HETATM 30 C C31 EQB . . . EA 17 57.085 -144.664 50.05 1 81.81 ? C31 EQB 301 H 1 
HETATM 31 C C32 EQB . . . EA 17 56.978 -143.575 50.88 1 84.85 ? C32 EQB 301 H 1 
HETATM 32 C C33 EQB . . . EA 17 57.074 -142.315 50.331 1 88.58 ? C33 EQB 301 H 1 
HETATM 33 C C34 EQB . . . EA 17 57.275 -142.162 48.972 1 94.62 ? C34 EQB 301 H 1 
#
_model_server_stats.io_time_ms              99 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    283 
_model_server_stats.query_time_ms           301 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           33 
#